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The electrocardiographic PR interval (or PQ interval) reflects atrial and atrioventricular nodal conduction, disturbances of which increase risk of atrial fibrillation. We report a meta-analysis of genome-wide association studies for PR interval from seven population-based European studies in the CHARGE Consortium: AGES, ARIC, CHS, FHS, KORA, Rotterdam(More)
MOTIVATION From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and(More)
BACKGROUND Identification of terms is essential for biomedical text mining.. We concentrate here on the use of vocabularies for term identification, specifically the Unified Medical Language System (UMLS). To make the UMLS more suitable for biomedical text mining we implemented and evaluated nine term rewrite and eight term suppression rules. The rules rely(More)
BACKGROUND AND OBJECTIVE In order for computers to extract useful information from unstructured text, a concept normalization system is needed to link relevant concepts in a text to sources that contain further information about the concept. Popular concept normalization tools in the biomedical field are dictionary-based. In this study we investigate the(More)
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 documents and associations for several classes of biomedical concepts, including genes, drugs and diseases, with established text-mining technology. In this(More)
There is a trend towards automatic analysis of large amounts of literature in the biomedical domain. However, this can be effective only if the ambiguity in natural language is resolved. In this paper, the current state of research in word sense disambiguation (WSD) is reviewed. Several methods for WSD have already been proposed, but many systems have been(More)
The CALBC initiative aims to provide a large-scale biomedical text corpus that contains semantic annotations for named entities of different kinds. The generation of this corpus requires that the annotations from different automatic annotation systems be harmonized. In the first phase, the annotation systems from five participants (EMBL-EBI, EMC Rotterdam,(More)
BACKGROUND Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck. RESULTS We developed a simple thesaurus-based disambiguation algorithm that can operate with very little training data. The thesaurus comprises the(More)
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 for large-cale and high-speed indexing. The thesaurus used for indexing was constructed as a combination of the MESH thesaurus and the gene ontology (GO), with a(More)