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Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all(More)
Genome sciences have experienced an increasing demand for efficient text-processing tools that can extract biologically relevant information from the growing amount of published literature. In response, a range of text-mining and information-extraction tools have recently been developed specifically for the biological domain. Such tools are only useful if(More)
Life-Cycle Engineering is a design methodology that takes into account the mutually constraining influences of product manufacturability, testability and maintainability as well as functionality. We are using non-directional constraint networks to model these mutually constraining influences in order to enable product designers to design more successful(More)
Morphological analysis as applied to English has generally involved the study of rules for inflections and derivations. Recent work has attempted to derive such rules from automatic analysis of corpora. Here we study similar issues, but in the context of the biological literature. We introduce a new approach which allows us to assign probabilities of the(More)
Chapter Overview In this chapter, an introductory description of the exploration of genomic data is given. Rather than attempt an exhaustive overview of the types of genomic data and methods of analysis, the chapter focuses on one type of data, gene expression profiling by microarray technology, and one method of analysis, cluster analysis for discovering(More)
The extraction of protein-protein interactions (PPIs) reported in scientific publications is one of the most studied topics in Text Mining in the Life Sciences, as such algorithms can substantially decrease the effort for databases curators. The currently best methods for this task are based on analyzing the dependency tree (DT) representation of sentences.(More)