Proposed minimum reporting standards for chemical analysis

There is a general consensus that supports the need for standardized reporting of metadata or information describing large-scale metabolomics and other functional genomics data sets. Reporting of standard metadata provides a biological and empirical context for the data, facilitates experimental replication, and enables the re-interrogation and comparison of data by others. Accordingly, the Metabolomics Standards Initiative is building a general consensus concerning the minimum reporting standards for metabolomics experiments of which the Chemical Analysis Working Group (CAWG) is a member of this community effort. This article proposes the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation, experimental analysis, quality control, metabolite identification, and data pre-processing. These minimum standards currently focus mostly upon mass spectrometry and nuclear magnetic resonance spectroscopy due to the popularity of these techniques in metabolomics. However, additional input concerning other techniques is welcomed and can be provided via the CAWG on-line discussion forum at or . Further, community input related to this document can also be provided via this electronic forum. The contents of this paper do not necessarily reflect any position of the Government or the opinion of the Food and Drug Administration Sponsor: Metabolomics Society http://www.metabolomicssociety.org/ Reference: http://msi-workgroups.sourceforge.net/bio-metadata/reporting/pbc/ http://msi-workgroups.sourceforge.net/chemical-analysis/ Version: Revision: 5.1 Date: 09 January, 2007     

Better chemistry for better survival,through regulation

In this issue of Cell, report on new aspects of the regulation of yeast ribonucleotide reductase, the mechanism by which dNTP levels are increased following DNA damage, and the consequences of the metabolic changes.     

Meta‐analysis shows that environmental DNA outperforms traditional surveys,but warrants better reporting standards

1. Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost‐effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta‐analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently “better.”
2. Environmental DNA publications for multiple species or single macro‐organism detection were identified using the Web of Science, by searching “eDNA” and “environmental DNA” across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.
3. Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa‐dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance.
4. Synthesis and applications: The results of this meta‐analysis demonstrate that where there is a direct comparison, eDNA surveys of macro‐organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods‐based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.

     

Proposed minimum reporting standards for data analysis in metabolomics

The goal of this group is to define the reporting requirements associated with the statistical analysis (including univariate, multivariate, informatics, machine learning etc.) of metabolite data with respect to other measured/collected experimental data (often called meta-data). These definitions will embrace as many aspects of a complete metabolomics study as possible at this time. In chronological order this will include: Experimental Design, both in terms of sample collection/matching, and data acquisition scheduling of samples through whichever spectroscopic technology used; Deconvolution (if required); Pre-processing, for example, data cleaning, outlier detection, row/column scaling, or other transformations; Definition and parameterization of subsequent visualizations and Statistical/Machine learning Methods applied to the dataset; If required, a clear definition of the Model Validation Scheme used (including how data are split into training/validation/test sets); Formal indication on whether the data analysis has been Independently Tested (either by experimental reproduction, or blind hold out test set). Finally, data interpretation and the visual representations and hypotheses obtained from the data analyses.     

Achievable standards, benchmarks for reporting and criteria for evaluating cervical cytopathology

Summary of the report of a working party set up by the Royal College of Pathologists, British Society for Clinical Cytology (BSCC) and NHS Cervical Screening Programme (NHSCSP) which is circulated with this issue of Cytopathology and is also available as an NHSCSP document.     

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.     

The ARRIVE guidelines,a welcome improvement to standards for reporting animal research

Here we introduce the ARRIVE (Animal Research: Reporting In Vivo Experiments) guidelines, produced by the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), which are published in this issue of the journal with our endorsement, and will be incorporated into our Instructions to Authors. Copyright © 2010 John Wiley & Sons, Ltd.     

The quality of reporting of RCTs used within a postoperative pain management meta-analysis, using the CONSORT statement

Background

Randomized controlled trials (RCTs) are routinely used in systematic reviews and meta-analyses that help inform healthcare and policy decision making. The proper reporting of RCTs is important because it acts as a proxy for health care providers and researchers to appraise the quality of the methodology, conduct and analysis of an RCT. The aims of this study are to analyse the overall quality of reporting in 23 RCTs that were used in a meta-analysis by assessing 3 key methodological items, and to determine factors associated with high quality of reporting. It is hypothesized that studies with larger sample sizes, that have funding reported, that are published in journals with a higher impact factor and that are in journals that have adopted or endorsed the CONSORT statement will be associated with better overall quality of reporting and reporting of key methodological items.

Methods

We systematically reviewed RCTs used within an anesthesiology related post-operative pain management meta-analysis. We included all of the 23 RCTs used, all of which were parallel design that addressed the use of femoral nerve block in improving outcomes after total knee arthroplasty. Data abstraction was done independently by two reviewers. The two main outcomes were: 1) 15 point overall quality of reporting score (OQRS) based on the Consolidated Standards for Reporting Trials (CONSORT) and 2) 3 point key methodological item score (KMIS) based on allocation concealment, blinding and intention-to-treat analysis.

Results

Twenty-three RCTs were included. The median OQRS was 9.0 (Interquartile Range?=?3). A multivariable regression analysis did not show any significant association between OQRS or KMIS and our four predictor variables hypothesized to improve reporting. The direction and magnitude of our results when compared to similar studies suggest that the sample size and impact factor are associated with improved key methodological item reporting.

Conclusions

The quality of reporting of RCTs used within an anesthesia related meta-analysis is poor to moderate. The information gained from this study should be used by journals to register the urgency for RCTs to be clear and transparent in reporting to help make literature accessible and comparable.     

Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results

Informatics standards and controlled vocabularies are essentialfor allowing information technology to help exchange, manage,interpret and compare large data collections. In a rapidly evolvingfield, the challenge is to work out how best to describe, butnot prescribe, the use of these technologies and methods. AMetabolomics Standards Workshop was held by the US NationalInstitutes of Health (NIH) to bring together multiple ongoingstandards efforts in metabolomics with the NIH research community.The goals were to discuss metabolomics workflows (methods, technologiesand data treatments) and the needs, challenges and potentialapproaches to developing a Metabolomics Standards Initiativethat will help facilitate this rapidly growing field which hasbeen a focus of the NIH roadmap effort. This report highlightsspecific aspects of what was presented and discussed at the1st and 2nd August 2005 Metabolomics Standards Workshop.      

The need for standards, not guidelines, in biological data reporting and sharing

Implementation of the Minimal information about a microarray experiment document provides several lessons for similar ongoing initiatives in other fields.