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Anni 2.0 is an online tool (http://biosemantics.org/anni/) to aid the biomedical researcher with a broad range of information needs. Anni provides an ontology-based interface to MEDLINE and retrieves… Continue Reading
To achieve high speed with minimal effort, we created a system dubbed Peregrine that performs gene name normalization by simple dictionary lookup followed by several post-processing steps.
BackgroundHigh throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological… Continue Reading
MOTIVATION Full-text documents potentially hold more information than their abstracts, but require more resources for processing. We investigated the added value of full text over abstracts in terms… Continue Reading
BackgroundHigh-throughput experiments, such as with DNA microarrays, typically result in hundreds of genes potentially relevant to the process under study, rendering the interpretation of these… Continue Reading
Genes are discovered almost on a daily basis and new names have to be found. Although there are guidelines for gene nomenclature, the naming process is highly creative. Human genes are often named… Continue Reading
BACKGROUND Text-mining has been used to link biomedical concepts, such as genes or biological processes, to each other for annotation purposes or the generation of new hypotheses. To relate two… Continue Reading
The Biosemantics group at the Erasmus MC followed a thesaurus-based approach for the first task of the genomics track. The approach is based on a concept-based indexing engine (Collexis®), suitable… Continue Reading
MOTIVATION The advent of high-throughput experiments in molecular biology creates a need for methods to efficiently extract and use information for large numbers of genes. Recently, the associative… Continue Reading
BackgroundComparative analysis of expression microarray studies is difficult due to the large influence of technical factors on experimental outcome. Still, the identified differentially expressed… Continue Reading