OMICS studies: How about metadata checklist and data publications?

[Quality control study of engineered skin tissue]

OMERO service was used to annotate the cell line HaCaT microscope images by two independent expert groups. The images were obtained in the course of developing tissue-engineered epithelium which consisted of several layers of the keratinocytes. Evaluation of expert opinions was performed by calculation of specificity, sensitivity and accuracy. The best convergence of opinions (91%) was achieved for the confluence of the cell monolayers. Accuracy 70% was observed in determining the extent of cell differentiation after 10 days of incubation. The paper illustrates the usefulness of OMERO service for dynamic cross-validation of quality in the development and standardization of cell preparations.

The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders

Complex diseases are caused by a combination of genetic and environmental factors, creating a difficult challenge for diagnosis and defining subtypes. This review article describes how distinct disease subtypes can be identified through integration and analysis of clinical and multi-omics data. A broad shift toward molecular subtyping of disease using genetic and omics data has yielded successful results in cancer and other complex diseases. To determine molecular subtypes, patients are first classified by applying clustering methods to different types of omics data, then these results are integrated with clinical data to characterize distinct disease subtypes. An example of this molecular-data-first approach is in research on Autism Spectrum Disorder (ASD), a spectrum of social communication disorders marked by tremendous etiological and phenotypic heterogeneity. In the case of ASD, omics data such as exome sequences and gene and protein expression data are combined with clinical data such as psychometric testing and imaging to enable subtype identification. Novel ASD subtypes have been proposed, such as CHD8, using this molecular subtyping approach. Broader use of molecular subtyping in complex disease research is impeded by data heterogeneity, diversity of standards, and ineffective analysis tools. The future of molecular subtyping for ASD and other complex diseases calls for an integrated resource to identify disease mechanisms, classify new patients, and inform effective treatment options. This in turn will empower and accelerate precision medicine and personalized healthcare.

Norms of data sharing in biological sciences: The roles of metadata, data repository, and journal and funding requirements

Institutional environments, comprising regulative pressures by funding agencies and journal publishers, and institutional resources, including the availabilities of data repositories and standards for metadata, function as important determinants in scientists’ data-sharing norms, attitudes and behaviours. This research investigates how these functions influence biological scientists’ data-sharing norms and how the data-sharing norms influence their data-sharing behaviours mediated by attitudes towards data sharing. The research model was developed based on the integration of institutional theory and theory of planned behaviour. The proposed research model was validated based on a total of 608 responses from a national survey conducted in the USA. The Partial Least Squares (PLS) was employed to analyse the survey data. Results show how institutional pressures by funding agencies and journals and the availabilities of data repository and metadata standards all have significant influences on data-sharing norms, which have significant influences on data-sharing behaviours, as mediated by attitudes towards data sharing.

The 'prime-ome': towards a holistic approach to priming

Plants can be primed to respond faster and more strongly to stress and multiple pathways, specific for the encountered challenge, are involved in priming. This adaptability of priming makes it difficult to pinpoint an exact mechanism: the same phenotypic observation might be the consequence of unrelated underlying events. Recently, details of the molecular aspects of establishing a primed state and its transfer to offspring have come to light. Advances in techniques for detection and quantification of elements spanning the fields of transcriptomics, proteomics, and metabolomics, together with adequate bioinformatics tools, will soon allow us to take a holistic approach to plant defence. This review highlights the state of the art of new strategies to study defence priming in plants and provides perspectives towards 'prime-omics'.