Do Editorial Policies Support Ethical Research? A Thematic Text Analysis of Author Instructions in Psychiatry Journals

Introduction: According to the Declaration of Helsinki and other guidelines, clinical studies should be approved by a research ethics committee and seek valid informed consent from the participants. Editors of medical journals are encouraged by the ICMJE and COPE to include requirements for these principles in the journal's instructions for authors. This study assessed the editorial policies of psychiatry journals regarding ethics review and informed consent. Methods and Findings: The information given on ethics review and informed consent and the mentioning of the ICMJE and COPE recommendations were assessed within author's instructions and online submission procedures of all 123 eligible psychiatry journals. While 54% and 58% of editorial policies required ethics review and informed consent, only 14% and 19% demanded the reporting of these issues in the manuscript. The TOP-10 psychiatry journals (ranked by impact factor) performed similarly in this regard. Conclusions: Only every second psychiatry journal adheres to the ICMJE's recommendation to inform authors about requirements for informed consent and ethics review. Furthermore, we argue that even the ICMJE's recommendations in this regard are insufficient, at least for ethically challenging clinical trials. At the same time, ideal scientific design sometimes even needs to be compromised for ethical reasons. We suggest that features of clinical studies that make them morally controversial, but not necessarily unethical, are analogous to methodological limitations and should thus be reported explicitly. Editorial policies as well as reporting guidelines such as CONSORT should be extended to support a meaningful reporting of ethical research.

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.