The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world

The amount of data currently being generated by proteomics laboratories around the world is increasing exponentially, making it ever more critical that scientists are able to exchange, compare and retrieve datasets when re-evaluation of their original conclusions becomes important. Only a fraction of this data is published in the literature and important information is being lost every day as data formats become obsolete. The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was tasked with the creation of data standards and interchange formats to allow both the exchange and storage of such data irrespective of the hardware and software from which it was generated. This article will provide an update on the work of this group, the creation and implementation of these standards and the standards-compliant data repositories being established as result of their efforts.     

eScience and the need for data standards in the life sciences: in pursuit of objectivity rather than truth

Referring to European history of natural sciences as an example, I discuss the relation between development of standards and the emergence of new epistemic virtues. I distinguish standards relating to scientific argumentation from standards relating to data production. The former are based on truth-seeking epistemic virtues and use criteria of logical coherence and empirical grounding. They are important for the justification of an explanatory hypothesis. Data and metadata standards, on the other hand, concern the data record itself and all steps and actions taken during data production and are based on virtues of objectivity. In the second part I focus on data and metadata standards and argue that, in order to meet the requirements of eScience, the specification of the currently popular minimum information checklists should be complemented to cover four aspects: (i) content standards, which increase reproducibility and operational transparency of data production, (ii) concept standards, which increase the semantic transparency of the terms used in data records, (iii) nomenclatural standards, which provide stable and unambiguous links between the terms used and their underlying definitions or their real referents, and (iv) format standards, which increase compatibility and computer-parsability of data records. I discuss the role of scientific terminology for standardizing data and the need for using semantically standardized and formalized data-reporting languages in the form of controlled vocabularies and ontologies for establishing content standards for data in the life sciences. Finally I comment on the necessity of community participation in the development and application of standards and in making data openly available.     

How useful are environmental safety standards in economics? — The example of safe minimum standards for protection of species

The use of environmental safety standards is being increasingly advocated, and economists are being increasingly required to adapt their policy models to take account of such standards, e.g. by the use of transferable environmental damage quotas. The use of these standards may be a consequence of a greater desire to achieve more sustainable development and preserve the natural wealth available to future generations. An important means to this goal is to preserve biodiversity and genetic variability. Safe minimum standards for conservation of wildlife have been suggested as a way to achieve this. Sometimes safe minimum standards for conservation of species are defined in terms of their minimum viable populations and their minimum habitat requirements. However, as a review of recent scientific literature indicates, these safe minimum standards are very uncertain.Environmental safety standards have been integrated into economics in a variety of ways, e.g. via constraints to ensure sustainability at the macro-level, via minimum safety standards necessary to ensure survival of species. Despite the commendable support which safe minimum standards appear to give for nature conservation, they involve conceptual problems and uncertainties as outlined in this paper. In fact, safe minimum standards for the conservation of species do not exist — no standard ensures the continued existence of any species. This is not to deny that an improvement in standards can up to a point increase the probability of survival of a species for a specified period of time. It implies that minimum standards need to be cast in terms of those required to achieve a particular probability of survival of the targeted species for a specified period. It may, however, be impossible to achieve the goal specified, e.g. the probability of survival of a species aimed for, may be greater than can be achieved for any attainable standard. In general, the paper makes it clear that standards suggested by natural scientists and others need to be subjected to careful serutiny before they can be used as a reliable basis for economic policy.     

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.     

碳足迹核算的国际标准概述与解析

各种层面上的碳足迹核算在全球气候变化控制领域得到了越来越多的关注。但是,这些关于碳足迹核算的相关国际标准繁多,彼此之间的关系复杂,不利于研究领域和工业界对这些标准进行应用与交流,限制了碳足迹核算的发展进度与深度。对目前已有的国际主要碳足迹核算标准及生命周期评价标准进行了整理,梳理出这些国际标准的一些基本特征,绘制了国际标准之间的关系图;并进一步从生命周期评价步骤的角度出发,解析了各种国际标准在这些阶段上的相关内容,以及每一个阶段上各标准相关规定中的不同特点及逻辑关系。对促进我国碳足迹核算相关研究与实践工作具有一定的理论与现实参考意义。     

The need to study the holobiome for gainful uses of endophytes

It is established that endophytes (bacteria and fungi) affect positively several traits of their host plants including growth, nutrient acquisition, and tolerance to abiotic and biotic stressors. Owing to this, endophytes are envisaged as a route to improve sustainable agricultural production. However, such effects of endophytes on crops although evident under lab conditions, are devoid of consistency under field conditions. The main reason for this could be the lack of our understanding of the functioning of the endophytes as a consortium within the plant (holobiome). It is essential to study the complex web of interactions which operate in the inner tissues of plants harboring endophytes. I highlight here, alluding to the work on foliar fungal endophytes, the importance of studying endophytes as a consortium rather than merely as one species in isolation to better appreciate their role in the plant holobiome. Such an approach should aid in harnessing the technological potential of endophytes.     

Data standards for proteomics: mitochondrial two-dimensional polyacrylamide gel electrophoresis data as a model system

Proteomics has emerged as a major discipline that led to a re-examination of the need for consensus and a nationally sanctioned set of proteomics technology standards. Such standards for databases and data reporting may be applied to two-dimensional polyacrylamide gel electrophoresis (2D PAGE) technology as a pilot project for assessing global and national needs in proteomics, and the role of the National Institute of Standards and Technology (NIST) and other similar standards and measurement organizations. The experience of harmonizing the heterogeneous data included in the Protein Data Bank (PDB) provides a paradigm for technology in an area where significant heterogeneity in technical detail and data storage has evolved. Here we propose an approach toward standardizing mitochondrial 2D PAGE data in support of a globally relevant proteomics consensus.     

On principles and standards in ecological restoration

The Society for Ecological Restoration (SER) has long debated how to define best practices. We argue that a principles‐first approach offers more flexibility for restoration practitioners than a standards‐based approach, is consistent with the developmental stage of restoration, and functions more effectively at a global level. However, the solution is not as simple as arguing that one approach to professional practice is sufficient. Principles and standards can and do operate effectively together, but only if they are coordinated in a transparent and systematic way. Effective professional guidance results when standards anchored by principles function in a way that is contextual and evolving. Without that clear relation to principles, the tendency to promote performance standards may lead to a narrowing of restoration practice and reduction in the potential to resolve very difficult and diverse ecological and environmental challenges. We offer recommendations on how the evolving project of restoration policy by SER and other agencies and organizations can remain open and flexible.     

Scientific basis for the Soviet and Russian radiofrequency standards for the general public

The former Soviet Union (USSR) and the USA were the first countries to introduce standards limiting exposure to radiofrequency (RF) fields. However, the exposure limits in the USSR standards were always much lower than those in the USA and other countries. The objective of this article is to provide a history of the development of the Soviet and Russian RF standards. In addition, we summarize the scientific evidence used to develop the original USSR RF and subsequent Russian public health standards, as well as the mobile telecommunications standard published in 2003, but we do not critique them. We also describe the protective approaches used by the Soviet and Russian scientists for setting their limits. A translation of the papers of the key studies used to develop their standards is available in the online version of this publication. Bioelectromagnetics 33:623–633, 2012. © 2012 Wiley Periodicals, Inc.     

Urgent need for consistent standards in functional enrichment analysis

Gene set enrichment tests (a.k.a. functional enrichment analysis) are among the most frequently used methods in computational biology. Despite this popularity, there are concerns that these methods are being applied incorrectly and the results of some peer-reviewed publications are unreliable. These problems include the use of inappropriate background gene lists, lack of false discovery rate correction and lack of methodological detail. To ascertain the frequency of these issues in the literature, we performed a screen of 186 open-access research articles describing functional enrichment results. We find that 95% of analyses using over-representation tests did not implement an appropriate background gene list or did not describe this in the methods. Failure to perform p-value correction for multiple tests was identified in 43% of analyses. Many studies lacked detail in the methods section about the tools and gene sets used. An extension of this survey showed that these problems are not associated with journal or article level bibliometrics. Using seven independent RNA-seq datasets, we show misuse of enrichment tools alters results substantially. In conclusion, most published functional enrichment studies suffered from one or more major flaws, highlighting the need for stronger standards for enrichment analysis.     

Cleanup standards for petroleum hydrocarbons. part 2. Case study comparisons of site‐specific cleanup standards with generic TPH standards

Many states across the U.S. use the total petroleum hydrocarbon (TPH) measurement as a regulatory tool for setting cleanup standards for underground storage tank sites and other petroleum‐related sites requiring cleanup. In Part 1 of this article (Michelsen and Petito Boyce, J. Soil Contam., 2(2): 109–124), alternative techniques and new methods for developing site‐specific cleanup standards for petroleum hydrocarbons were reviewed, including the use of chemical fingerprinting, constituent analysis, and human health and ecological risk assessment methods. In Part 2 of this article, the cost effectiveness and accuracy of these approaches are evaluated by comparing a generic TPH cleanup standards approach with site‐specific cleanup standards approaches for two actual sites in Washington State, a neighborhood gas station and a former bulk fuel storage facility. Based on these case studies, as well as consideration of other available approaches discussed in Part 1 of this article, recommendations are provided for selecting the most appropriate method of developing cleanup standards at a petroleum‐contaminated site.     

Standards for biodiversity: a proposal based on biodiversity standards for forest plantations

The 1992 Convention on Biological Diversity has not only focused attention on the concept of biodiversity it has also set expectations that the signatory nations will establish objectives. It is suggested here that the use of biodiversity standards could have a useful role in quantifying these objectives. The use of biodiversity standards is explored in connection with the levels of biodiversity In plantation forests. Forest plantations have been used for the basis of this investigation because such plantations could be used as large-scale experiments in which the use of standards, and the ecological monitoring of these standards, could be researched. The impact of intensive forestry practices on wildlife has often been the cause of concern and indeed controversy. Recently there has been a move towards the development of multipurpose forest plantations where management for recreation and wildlife takes place alongside management for timber. Some forest authorities are actively looking at ways of restoring levels of biodiversity in plantation forests. We suggest that if levels of biodiversity are to be restored, then forest managers must have something to aim for; that is, there must be a standard. The adoption of standards could provide a means whereby forest managers can meet biodiversity objectives. Standards may also enable managers to determine the effectiveness of those management practices which are intended to increase levels of biodiversity. We suggest a conceptual plan which combines a monitoring procedure with biodiversity objectives.     

The need of specific standards for head dimensions of urban Sardinian boys

In the 1997-1998 and 1998-1999 school years we measured head dimensions of 1600 boys from 6 to 13 years attending elementary and middle schools in towns of the Cagliari area (Sardinia, Italy). For each age, we compared the mean values for circumference, length and width of the head with Canadian standards, widely used by Sardinian pediatricians. The t-test shows that the means of the three variables are significantly lower in the Cagliari boys than in their Canadian contemporaries, with the exception of head circumference in 6 and 7 year-olds, and of head width in 10 year-olds. Therefore, it is necessary to produce specific growth charts for circumference, length and width of the head of Sardinian children rather than evaluate their growth using standards of populations with different ethnic, geographical and socio-economic backgrounds.     

Basic data standards for primate colonies

A set of simple standards has been developed to ease the task of transferring primate colony data between institutions and computers, and to assure that colony vital statistics are appropriate for demographic and genetic analyses. The standards have been designed to be easily and inexpensively implemented from existing databases, and also may serve as a guide to the setup of new colony record-keeping systems. © 1993 Wiley-Liss, Inc.     

Medical and non-medical protection standards for ultrasound and infrasound

Protection from inappropriate or hazardous exposure to ultrasound is controlled through international standards and national regulations. IEC standard 60601 part 1 establishes requirements for the mechanical, electrical, chemical and thermal safety for all electro-medical equipment. The associated part 2 standard for diagnostic medical ultrasonic equipment sets no upper limits on ultrasonic exposure. Instead, safety indices are defined that are intended to advise users on the degree of thermal and mechanical hazard. At present the display of these safety indices satisfies regulatory requirements in both the USA and Europe. Nevertheless there are reservations about the effectiveness of this approach to protection management. In the USA, there are national regulatory limits on diagnostic exposure, based on acoustic output from clinical equipment in use over 20 years ago. The IEC 60601 part 2 standard for therapeutic equipment sets 3 W cm⁻² as the limit on acoustic intensity. Transducer surface temperature is controlled for both diagnostic and therapy devices.

For airborne ultrasound, interim guidelines on limits of human exposure published by the IRPA are now 2 decades old. A limit on sound pressure level of 100 dB for the general population is recommended. The absence of protection standards for infrasound relates to difficulties in measurement at these low frequencies.     

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.     

Analysis and regulation of legume inoculants in Canada: The need for an increase in standards

Herbicide residues may affect seedlings during early stages of their development. We studied this possibility by the use of light and electron microscopy after incubation of germinating seeds ofPisum sativum L. andZea mays L. with different concentrations of chlorsulfuron and metsulfuron-methyl. By in vitro experiments, we have shown that both herbicides caused growth reduction of the very young roots, and severe ultrastructural alterations and injuries of the root caps of both species. Chlorsulfuron caused increase of electron-dense material in the vacuoles, cytoplasmic degeneration even in the inner secretory cell layers of the cap, and disruption of the amyloplast envelopes with release of the statolithic starch grains. In the initial cell complex of the root cap, the herbicides caused the formation of large concentric aggregates of the rough ER and wall disformations in the cells adjacent to this complex. Scanning electron microscopic observations revealed a decrease of the slime layer ensheathing the root cap and the subapical root surface.We conclude that even in early stages of seed germination, both herbicides seriously affect the gravity perception centre (consisting of the statocytes), and the secretory tissue of the root caps, thus probably disturbing the processes of gravitropism and the protective slime secretion of the roots.