LINNAEUS: A species name identification system for biomedical literature

• Main Authors: Nenadic Goran, Gerner Martin, Bergman Casey M
• Format: Article
• Language: English
• Published: BMC 2010-02-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/11/85

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 mentions. When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level. Our system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers.</p> <p>Conclusions</p> <p>LINNAEUS is an open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and text-mining applications. The software and manually annotated corpus can be downloaded freely at <url>http://linnaeus.sourceforge.net/</url>.</p>