BackgroundBiomedical knowledge bases (KB’s) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at which new findings are published. Second, for automatic information extraction (IE), the text genre of choice has been scientific publications, neglecting sources like health portals and online communities. Third, most prior work on IE has focused on the molecular level or chemogenomics only, like protein-protein interactions or gene-drug relationships, or solely address highly specific topics such as drug effects.ResultsWe address these three limitations by a versatile and scalable approach to automatic KB construction. Using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a huge number of facts in an automated manner without requiring any explicit training.We extend previous techniques for pattern-based IE with confidence statistics, and we combine this recall-oriented stage with logical reasoning for consistency constraint checking to achieve high precision. To our knowledge, this is the first method that uses consistency checking for biomedical relations. Our approach can be easily extended to incorporate additional relations and constraints.We ran extensive experiments not only for scientific publications, but also for encyclopedic health portals and online communities, creating different KB’s based on different configurations. We assess the size and quality of each KB, in terms of number of facts and precision. The best configured KB, KnowLife, contains more than 500,000 facts at a precision of 93% for 13 relations covering genes, organs, diseases, symptoms, treatments, as well as environmental and lifestyle risk factors.ConclusionKnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from different text genres such as scientific publications, health portals, and online communities. Thus, it has the potential to serve as one-stop portal for a wide range of relations and use cases. To showcase the breadth and usefulness, we make the KnowLife KB accessible through the health portal (http://knowlife.mpi-inf.mpg.de).Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0549-5) contains supplementary material, which is available to authorized users.

Automatic translation of documents is an important task in many domains, including the biological and clinical domains. The second edition of the Biomedical Translation task in the Conference of Machine Translation focused on the automatic translation of biomedical-related documents between English and various European languages. This year, we addressed ten languages: Czech, German, English, French, Hungarian, Polish, Portuguese, Spanish, Romanian and Swedish. Test sets included both scientific publications (from the Scielo and EDP Sciences databases) and health-related news (from the Cochrane and UK National Health Service web sites). Seven teams participated in the task, submitting a total of 82 runs. Herein we describe the test sets, participating systems and results of both the automatic and manual evaluation of the translations.

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The author list is alphabetical and does not reflect the respective author contributions. The task was coordinated by Mariana Neves. sions were judged to be better than the reference translations, for instance, for de/en, en/es and es/en. 10 https://github.com/glample/fastBPE 11 1 encoder layer, 1 decoder layer, both with with GRU cells, embedding dimension of 512, hidden state of dimension 1024, using layer normalization, implemented using Marian NMT and trained using the Adam optimizer.

Machine translation enables the automatic translation of textual documents between languages and can facilitate access to information only available in a given language for nonspeakers of this language, e.g. research results presented in scientific publications. In this paper, we provide an overview of the Biomedical Translation shared task in the Workshop on Machine Translation (WMT) 2018, which specifically examined the performance of machine translation systems for biomedical texts. This year, we provided test sets of scientific publications from two sources (EDP and Medline) and for six language pairs (English with each of Chinese, French, German, Portuguese, Romanian and Spanish). We describe the development of the various test sets, the submissions that we received and the evaluations that we carried out. We obtained a total of 39 runs from six teams and some of this year's BLEU scores were somewhat higher that last year's, especially for teams that made use of biomedical resources or state-of-the-art MT algorithms (e.g. Transformer). Finally, our manual evaluation scored automatic translations higher than the reference translations for German and Spanish.