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Current advances in high-throughput biology are accompanied by a tremendous increase in the number of related publications. Much biomedical information is reported in the vast amount of literature. The ability to rapidly and effectively survey the literature is necessary for both the design and the interpretation of large-scale experiments, and for curation of structured biomedical knowledge in public databases. Given the millions of published documents, the field of information retrieval, which is concerned with the automatic identification of relevant documents from large text collections, has much to offer. This paper introduces the basics of information retrieval, discusses its applications in biomedicine, and presents traditional and non-traditional ways in which it can be used. [ABSTRACT FROM AUTHOR]

The process of building a new database relevant to some field of study in biomedicine involves transforming, integrating and cleansing multiple data sources, as well as adding new material and annotations. This paper reviews some of the requirements of a general solution to this data integration problem. Several representative technologies and approaches to data integration in biomedicine are surveyed. Then some interesting features that separate the more general data integration technologies from the more specialised ones are highlighted. [ABSTRACT FROM AUTHOR]

Summary: A review of the recent literature on treatment modalities of adult thoracic empyema was conducted in order to expose the controversies and verify where consensus exists. Critical reading filtered through clinical experience was the method followed. The roles of surgical drainage, lavage techniques, debridement via VATS, decortication, thoracoplasty and open window thoracostomy were considered using the Oxford Center of Evidence Based Medicine criteria. The roles of the different therapeutical modalities were interpreted in the light of the triphasic nature of empyema thoracis. The randomised controlled trials came up with conflicting results. With two exceptions all of the papers reviewed provide level (2b) or below evidences. The lack of a single ideal treatment modality or policy reflects the complexity of the diagnosis and staging of this heterogeneous disease. Basic elements of intervention – drainage, different evacuation techniques, decortication, thoracoplasty and open window thoracostomy – are well-established technical modalities; however, neither a universally acceptable primary modality nor the gold standard of their sequence is available. Drainage remains to be the initial treatment modality in Phase I disease. Debridement via VATS is a safe, reliable and efficient method in the fibrinopurulent phase. Organised pleural callus requires formal decortication. Open window thoracostomy is a simple and safe procedure for high-risk patients and results in quick detoxication. Thoracoplasty kept its final role in pleural space management. Acute postoperative bronchial stump insufficiency requires immediate surgery. Evacuation of toxic material is mandatory. No single-stage procedure offers a solution. An optimised agressivity treatment modality should be tailored to the condition of the patient and to the potential of the persisting cavity. Decision-making involves a triad consisting of the aetiology of empyema (i.e. primary vs secondary), general condition of the patient and stage of disease, while considering the triphasic nature of development of thoracic empyema. The current attitudes show that the present concepts are based mainly on expert opinion. Flexibility and patience on behalf of the surgeon and nursing staff, the patient and the hospital management, as well as a good understanding of the complexity of this condition are the cornerstones of the treatment. No exclusive sequence of procedures leading to a uniformly predictable successful outcome is available. Individualised approaches can be recommended based on institutional practice and local protocols. Thoracic empyema in general seems to remain resilient to fit completely into the categories of evidence-based medical approach. [Copyright &y& Elsevier]

Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and methods from diverse disciplines such as information management, knowledge representation, cognitive science, linguistics and philosophy. Depending on the desired applications in which ontologies are being applied, the evaluation of research in biomedical ontologies must follow different strategies. Here, we provide a classification of research problems in which ontologies are being applied, focusing on the use of ontologies in basic and translational research, and we demonstrate how research results in biomedical ontologies can be evaluated. The evaluation strategies depend on the desired application and measure the success of using an ontology for a particular biomedical problem. For many applications, the success can be quantified, thereby facilitating the objective evaluation and comparison of research in biomedical ontology. The objective, quantifiable comparison of research results based on scientific applications opens up the possibility for systematically improving the utility of ontologies in biomedical research. [ABSTRACT FROM PUBLISHER]

Reports on news pertaining to the biological sciences. Agreement signed between PPG Industries and Scripps Clinic; Donald F. Steiner who was awarded the Wolf Prize in Medicine; James R. Estes who was elected president of the American Society of Plant Taxonomists (ASPT); Neil A. Harrisman who was appointed the secretary of the ASPT.