Overview of BioCreAtIvE task 1B: normalized gene lists

Background: Our goal in BioCreAtIve has been to assess the state of the art in text mining, with emphasis on applications that reflect real biological applications, e.g., the curation process for model organism databases. This paper summarizes the BioCreAtIvE task 1B, the "Normalized Gene List" task, which was inspired by the gene list supplied for each curated paper in a model organism database. The task was to produce the correct list of unique gene identifiers for the genes and gene mentioned in sets of abstracts from three model organisms (Yeast, Fly, and Mouse). Results: Eight groups fielded systems for three data sets (Yeast, Fly, and Mouse). For Yeast, the top scoring system (out of 15) achieved 0.92 F-measure (harmonic mean of precision and recall); for Mouse and Fly, the task was more difficult, due to larger numbers of genes, more ambiguity in the gene naming conventions (particularly for Fly), and complex gene names (for Mouse). For Fly, the top F-measure was 0.82...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Lynette Hirschman, Marc E. Colosimo, Alexander A. Morgan, Alexander S. Yeh
• Keywords: BMCBI 2005, Gene, Gene List, Model Organism Databases