Metabolomics, in particular gas chromatography-mass spectrometry (GC-MS) based metabolite profiling of biological extracts, is rapidly becoming one of the cornerstones of functional genomics and systems biology. Metabolite profiling has profound applications in discovering the mode of action of drugs or herbicides, and in unravelling the effect of altered gene expression on metabolism and organism performance in biotechnological applications. As such the technology needs to be available to many laboratories. For this, an open exchange of information is required, like that already achieved for transcript and protein data. One of the key-steps in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations from biological samples. Collections of mass spectra, which comprise frequently observed metabolites of either known or unknown exact chemical structure, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here we present GMD, The Golm Metabolome Database, an open access metabolome database, which should enable these processes. GMD provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. with regard to methods, spectral information or compounds. The main goal will be the representation of an exchange platform for experimental research activities and bioinformatics to develop and improve metabolomics by multidisciplinary cooperation. AVAILABILITY: http://csbdb.mpimp-golm.mpg.de/gmd.html CONTACT: [email protected] SUPPLEMENTARY INFORMATION: http://csbdb.mpimp-golm.mpg.de/ (+info)
Ethics and scientific publication.
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This article summarizes the major categories of ethical violations encountered during submission, review, and publication of scientific articles. We discuss data fabrication and falsification, plagiarism, redundant and duplicate publication, conflict of interest, authorship, animal and human welfare, and reviewer responsibility. In each section, pertinent historical background and citation of relevant regulations and statutes are provided. Furthermore, a specific case(s) derived from actual situations is(are) presented. These cases were chosen to highlight the complexities that investigators and journals must face when dealing with ethical issues. A series of discussion questions follow each case. It is our hope that by increasing education and awareness of ethical matters relevant to scientific investigation and publication, deviations from appropriate conduct will be reduced. (+info)
Faculty statement from the CEU on a new publication: WHO Selected Practice Recommendations for Contraceptive Use Update. Missed pills: new recommendations.
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The World Health Organisation Selected Practice Recommendations for Contraceptive Use (WHOSPR) was first published in 2002 and provides evidence-based recommendations on how to use contraception effectively. The WHOSPR was adapted for UK use by the Faculty of Family Planning and Reproductive Heath Care (FFPRHC). The UK version is available on the FFPRHC website (www.ffprhc.org). Extensive field experience with the first edition of the WHOSPR highlighted to the WHO the need for revised recommendations for missed combined oral contraceptive pills (COCs). The WHOSPR was updated in 2004 and revised guidance on missed pills published. This guidance is now available on the WHO website (www.who.int/reproductive-health). The FFPRHC endorses the new recommendations from WHO on missed COCs for the following reasons: There is new evidence on which to base guidance. The WHOSPR follow a published and rigorous process for assessing the available evidence. The recommendations were developed by an international expert panel, with UK representation. Field experience shows a need for simple, harmonised guidance. This Statement summarises the revised WHOSPR evidence-based 'missed pill rules' in formats which we hope clinicians will find useful. We recognise that different individuals favour different styles for the presentation of information. Thus, both tabular and flow chart styles of summary are provided; these convey the same information but in different ways. The FFPRHC considers that the following statements may also serve as useful aides memoir for the 'missed pill rules': Whenever a woman realises that she has missed pills, the essential advice is 'just keep going'. She should take a pill as soon as possible and then resume her usual pill-taking schedule. Also, if the missed pills are in week three, she should omit the pill-free interval. Also, a back-up method (usually condoms) or abstinence should be used for 7 days if the following numbers of pills are missed: 'Two for twenty' (ie if two or more 20 microgram ethinylestradiol pills are missed). 'Three for thirty' (ie if three or more 30-35 microgram ethinylestradiol pills are missed). The fpa (Family Planning Association) has produced a revised COC user information sheet to reflect these changes; available from April 2005. (+info)
The medical students' societies and medical students' publications.
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The rich corporate life of the medical student and the medical students' societies at our medical school (at the present National University of Singapore) is generally unappreciated by its graduates and regrettably, even more unknown to the medical student of today. The present generation of medical students of NUS do not know of their rich history. We have published documentation of student activities from the founding of the medical school in 1905 till the establishment of the then University of Malaya in 1950, reviewed herein. Materials presented after 1950 were gathered from personal communications from key players in the students' societies and from editors of the medical students' publications. (+info)
Presentation and subsequent publication rates of phase I oncology clinical trials.
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BACKGROUND: Many trials submitted to scientific meetings are not reported in peer-reviewed journals. Results may vary substantially and the lack of final publication constitutes a form of reporting bias. The authors sought to determine the presentation and publication rates of Phase I trials submitted to a major oncology meeting and the factors impeding their subsequent publication. METHODS: The authors identified all Phase I studies submitted to the annual meeting of the American Society of Clinical Oncology in 1997, categorizing them as novel (agents not approved by the Food and Drug Administration at the time of submission) or nonnovel (at least one agent approved), and as industry sponsored or not. MEDLINE searches and an E-mailed questionnaire confirmed publication in peer-reviewed literature and the reasons for nonpublication. RESULTS: Approximately 54% of the 275 Phase I studies were selected for presentation. Abstracts reporting novel agents were more likely selected for presentation than those reporting nonnovel compounds (68% vs. 38%; P < 0.0001). Seventy-two percent of the presented abstracts were subsequently published, compared with 62% of those not presented (P = 0.08). The overall publication rate was 67% at 7.5 years. Presentation status was associated with time to publication (P = 0.01), with abstracts chosen for presentation being published sooner. The median time from presentation to publication was found to be 3.4 years. Lack of time and author relocation were the major obstacles to publication. CONCLUSIONS: The underreporting of final results of Phase I oncology trials remains a serious problem. In the future, investigators must commit to the publication of final results in a timely manner. Journals should provide mechanisms for rapid reporting of Phase I trials. (+info)
Balance between education- and research-oriented publications from a Brazilian University Hospital.
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We analyzed the trends of scientific output of the University Hospital, Federal University of Rio de Janeiro. A total of 1420 publications were classified according to pattern and visibility. Most were non-research publications with domestic visibility. With time, there was a tendency to shift from non-research (or education-oriented) publications with domestic visibility to research publications with international visibility. This change may reflect new academic attitudes within the institution concerning the objectives of the hospital and the establishment of scientific research activities. The emphasis of this University Hospital had been on the training of new physicians. However, more recently, the production of new knowledge has been incorporated as a new objective. The analysis of the scientific production of the most productive sectors of the hospital also showed that most are developing non-research studies devoted to the local public while a few of the sectors are carrying out research studies published in journals with international status. The dilemma of quality versus quantity and of education versus research-oriented publication seems, however, to continue to exist within the specialized sectors. The methodology described here to analyze the scientific production of a university hospital can be used as a tool to better understand the evolution of medical research in Brazil and also to help formulate public policies and new strategies to include research among the major objectives of University Hospitals. (+info)
Reducing workload in systematic review preparation using automated citation classification.
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OBJECTIVE: To determine whether automated classification of document citations can be useful in reducing the time spent by experts reviewing journal articles for inclusion in updating systematic reviews of drug class efficacy for treatment of disease. DESIGN: A test collection was built using the annotated reference files from 15 systematic drug class reviews. A voting perceptron-based automated citation classification system was constructed to classify each article as containing high-quality, drug class-specific evidence or not. Cross-validation experiments were performed to evaluate performance. MEASUREMENTS: Precision, recall, and F-measure were evaluated at a range of sample weightings. Work saved over sampling at 95% recall was used as the measure of value to the review process. RESULTS: A reduction in the number of articles needing manual review was found for 11 of the 15 drug review topics studied. For three of the topics, the reduction was 50% or greater. CONCLUSION: Automated document citation classification could be a useful tool in maintaining systematic reviews of the efficacy of drug therapy. Further work is needed to refine the classification system and determine the best manner to integrate the system into the production of systematic reviews. (+info)
MachineProse: an ontological framework for scientific assertions.
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OBJECTIVE: The idea of testing a hypothesis is central to the practice of biomedical research. However, the results of testing a hypothesis are published mainly in the form of prose articles. Encoding the results as scientific assertions that are both human and machine readable would greatly enhance the synergistic growth and dissemination of knowledge. DESIGN: We have developed MachineProse (MP), an ontological framework for the concise specification of scientific assertions. MP is based on the idea of an assertion constituting a fundamental unit of knowledge. This is in contrast to current approaches that use discrete concept terms from domain ontologies for annotation and assertions are only inferred heuristically. MEASUREMENTS: We use illustrative examples to highlight the advantages of MP over the use of the Medical Subject Headings (MeSH) system and keywords in indexing scientific articles. RESULTS: We show how MP makes it possible to carry out semantic annotation of publications that is machine readable and allows for precise search capabilities. In addition, when used by itself, MP serves as a knowledge repository for emerging discoveries. A prototype for proof of concept has been developed that demonstrates the feasibility and novel benefits of MP. As part of the MP framework, we have created an ontology of relationship types with about 100 terms optimized for the representation of scientific assertions. CONCLUSION: MachineProse is a novel semantic framework that we believe may be used to summarize research findings, annotate biomedical publications, and support sophisticated searches. (+info)