Metabolomics standards initiative: ontology working group work in progress

In this article we present the activities of the Ontology Working Group (OWG) under the Metabolomics Standards Initiative (MSI) umbrella. Our endeavour aims to synergise the work of several communities, where independent activities are underway to develop terminologies and databases for metabolomics investigations. We have joined forces to rise to the challenges associated with interpreting and integrating experimental process and data across disparate sources (software and databases, private and public). Our focus is to support the activities of the other MSI working groups by developing a common semantic framework to enable metabolomics-user communities to consistently annotate the experimental process and to enable meaningful exchange of datasets. Our work is accessible via a public webpage and a draft ontology has been posted under the Open Biological Ontology umbrella. At the very outset, we have agreed to minimize duplications across omics domains through extensive liaisons with other communities under the OBO Foundry. This is work in progress and we welcome new participants willing to volunteer their time and expertise to this open effort. See the MSI Ontology Working Group website for a complete list of members and contributors. Web URL:     

The establishment of China's core biodiversity metadata standard

Biodiversity metadata provide service to query, management and use of actual data sets. The progress of the development of metadata standards in China was analyzed, and metadata required and/or produced based on the Convention on Biological Diversity were reviewed. A biodiversity metadata standard was developed based on the characteristics of biodiversity data and in line with the framework of international metadata standards. The content of biodiversity metadata is divided into two levels. The first level consists of metadata entities and elements that are necessary to exclusively identify a biodiversity data set, and is named as Core Metadata. The second level comprises metadata entities and elements that are necessary to describe all aspects of a biodiversity data set. The standard for core biodiversity metadata is presented in this paper, which is composed of 51 elements belonging to 6 categories (entities), i.e. inventory information, collection information, information on the content of the data set, management information, access information, and metadata management information. The name, definition, condition, data type, and field length of metadata elements in these six categories (entities) are also described.     

Minimum reporting standards for plant biology context information in metabolomic studies

Plant metabolomics has matured over the past 8 years. Plant biologists routinely use comprehensive analyses of plant metabolites to discover new responses to genetic or environmental perturbation, or to validate initial hypotheses on the function and in vivo action of gene products. The wealth of scientific findings has increasingly provoked interest to share and review raw or processed data from plant metabolomics reports. We here suggest a minimum of parameters to be reported in order to define details of experimental study designs in plant metabolomics studies.     

Automated cryoEM data acquisition and analysis of 284742 particles of GroEL

One of the goals in developing our automated electron microscopy data acquisition system, Leginon, was to improve both the ease of use and the throughput of the process of acquiring low dose images of macromolecular specimens embedded in vitreous ice. In this article, we demonstrate the potential of the Leginon system for high-throughput data acquisition by describing an experiment in which we acquired images of more than 280,000 particles of GroEL in a single 25 h session at the microscope. We also demonstrate the potential for an automated pipeline for molecular microscopy by showing that these particles can be subjected to completely automated procedures to reconstruct a three-dimensional (3D) density map to a resolution better than 8 A. In generating the 3D maps, we used a variety of metadata associated with the data acquisition and processing steps to sort and select the particles. These metadata provide a number of insights into factors that affect the quality of the acquired images and the resulting reconstructions. In particular, we show that the resolution of the reconstructed 3D density maps improves with decreasing ice thickness. These data provide a basis for assessing the capabilities of high-throughput macromolecular microscopy.     

Integrative exposure assessment through classification and regression trees on bioaccumulation of metals, related sampling site characteristics and ecoregions

The UNECE Heavy Metals in Mosses Surveys measure and spatially predict environmental concentration (PEC) of metals in mosses for ecotoxicological risk assessments. Up to now, no statistical sound investigation was dedicated to those boundary conditions which, aside from the atmospheric depositions of metals from the atmosphere down to the land surface, might influence the bioaccumulation of metals. Thus, the article focuses on the integrative analysis of the data on the bioaccumulation of metals in Germany 1990, 1995 and 2000 on the one hand and of data on conceivable boundary conditions on the other hand. To this end Classification and Regression Trees (CART) were used because CART is a very powerful statistical technique that enables to uncover structures in large data sets containing categorical and continuous data without any transformation of scale dignity. Within the framework of the Metals in Mosses Surveys, moss samples were taken at 592 sites in 1990, at 1026 sites in 1995 and at 1028 sites in 2000 in Germany. At each of them mosses were sampled and the concentrations of up to 40 metals were measured. The sampling, the ecological characteristics of the sampling sites, and the chemical analysis were documented in a metadata base. An ecoregionalisation of Germany was calculated with data on natural vegetation, altitude, soil texture and climate by means of CART. The ecoregions were mapped by GIS and intersected with multi-metal bioaccumulation indices calculated from the monitoring data 1990, 1995 and 2000. These indices were calculated by percentile statistics and the concentrations of As, Cd, Cr, Cu, Fe, Hg, Ni, Pb, V and Zn were integrated. To reach an integrative exposure assessment, for each survey a CART-model was computed encompassing the multi-metal bioaccumulation indices, the metadata and the ecoregionalization. The models describe the multivariate correlations of metal bioaccumulation with site-specific and ecoregional characteristics in a comprehensive and holistic manner over time, space and metal species. This is of crucial importance for the next step in ecological risk assessment, i.e. the interpretation of the exposure data with regard to predicted no effect concentrations (PNEC) and the sensitivity of ecosystems.