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In European research today, mobility has become firmly entrenched as a pre requisite for a successful scientific career; however, the reasons behind this emphasis on scientific nomadism are far from obvious. It is all too common for science policy-makers and funding bodies to extol the seemingly endless virtues of mobility, but it nearly amounts to heresy(More)
Text-mining algorithms make mistakes in extracting facts from natural-language texts. In biomedical applications, which rely on use of text-mined data, it is critical to assess the quality (the probability that the message is correctly extracted) of individual facts--to resolve data conflicts and inconsistencies. Using a large set of almost 100,000 manually(More)
We have generated and made publicly available two very large networks of molecular interactions: 49,493 mouse-specific and 52,518 human-specific interactions. These networks were generated through automated analysis of 368,331 full-text research articles and 8,039,972 article abstracts from the PubMed database, using the GeneWays system. Our networks cover(More)
Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical data within the pharmaceutical industry. Traditional architectures, based on monolithic applications, do not offer sufficient flexibility for a wide range of(More)
We describe a new tool for visualization of biomedical scientific trends. The method captures variations in scientific impact over time to allow for a comparison of relative significance and evolution of fields similar to a financial market scorecard. The tool is available at SciTrends (http://www.scitrends.net), depicting the evolution of almost 200(More)
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to(More)
Methods in biomedical text mining Methods to improve text mining of molecular biology interactions are needed to capture a richer information space and qualify the quality of extraction. Simple interaction models fail to describe contextual and confidence information that would help with more fine-grained analyses. Herein a method is presented to streamline(More)