Open access :an opportunity for biomedical research

Open access within the scientific community depends on the scientific context and the practices of the field. In the biomedical domain, the communication of research results is characterised by the importance of the peer reviewing process, the existence of a hierarchy among journals and the transfer of copyright to the editor. Biomedical publishing has become a lucrative market and the growth of electronic journals has not helped lower the costs. Indeed, it is difficult for today's public institutions to gain access to all the scientific literature. Open access is thus imperative, as demonstrated through the positions taken by a growing number of research funding bodies, the development of open access journals and efforts made in promoting open archives. This article describes the setting up of an Inserm portal for publication in the context of the French national protocol for open-access self-archiving and in an international context.     

BioTorrents: A File Sharing Service for Scientific Data

The transfer of scientific data has emerged as a significant challenge, as datasets continue to grow in size and demand for open access sharing increases. Current methods for file transfer do not scale well for large files and can cause long transfer times. In this study we present BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. BioTorrents is available at http://www.biotorrents.net.     

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals

Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38% had a data policy, 22% had a code policy, and 66% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16% in the number of data policies, a 30% increase in code policies, and a 7% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals.     

Lifting Industrial Ecology Modeling to a New Level of Quality and Transparency: A Call for More Transparent Publications and a Collaborative Open Source Software Framework

Industrial ecology (IE) is a maturing scientific discipline. The field is becoming more data and computation intensive, which requires IE researchers to develop scientific software to tackle novel research questions. We review the current state of software programming and use in our field and find challenges regarding transparency, reproducibility, reusability, and ease of collaboration. Our response to that problem is fourfold: First, we propose how existing general principles for the development of good scientific software could be implemented in IE and related fields. Second, we argue that collaborating on open source software could make IE research more productive and increase its quality, and we present guidelines for the development and distribution of such software. Third, we call for stricter requirements regarding general access to the source code used to produce research results and scientific claims published in the IE literature. Fourth, we describe a set of open source modules for standard IE modeling tasks that represent our first attempt at turning our recommendations into practice. We introduce a Python toolbox for IE that includes the life cycle assessment (LCA) framework Brightway2, the ecospold2matrix module that parses unallocated data in ecospold format, the pySUT and pymrio modules for building and analyzing multiregion input‐output models and supply and use tables, and the dynamic_stock_model class for dynamic stock modeling. Widespread use of open access software can, at the same time, increase quality, transparency, and reproducibility of IE research.     

Fostering diffusion of scientific contents of National Society Cardiovascular Journals:the new ESC search engine

European Society of Cardiology (ESC) National Society Cardiovascular Journals (NSCJs) are high-quality biomedical journals focused on cardiovascular diseases. The Editors’ Network of the ESC devises editorial initiatives aimed at improving the scientific quality and diffusion of NSCJ. In this article we will discuss on the importance of the Internet, electronic editions and open access strategies on scientific publishing. Finally, we will propose a new editorial initiative based on a novel electronic tool on the ESC web-page that may further help to increase the dissemination of contents and visibility of NSCJs.     

Political and social drivers for access to the countryside: the need for research on birds and recreational disturbance

The introduction of a statutory right of access to open country and registered common land in England and Wales in 2005 was a major milestone in a campaign traceable to the 19th century, with views strongly polarized between social classes and political parties, and between land owners and campaigners. More recently, access has also been recognized as a factor contributing to quality-of-life, public health, social diversity and rural economic issues. The mapping of access land revealed that 55% of it is also designated Site of Special Scientific Interest, where wildlife is legally conserved. This has generated a need to assess the implications of access in each case, and take measures to ensure nationally and internationally important features are protected, drawing on sound scientific principles. Early research, although competently undertaken, often failed to address population-scale effects significant at the designated-site level, enabling disputes and polarized 'beliefs' to be articulated. Hence, in addition to drawing up formal and transparent procedures for evaluating impacts and resolving difficulties, funds were released and a major programme initiated, commissioning applied research of direct relevance to the implementation of the legislation. This has pushed forward the boundaries of knowledge in a field which is both difficult and expensive to study. By gradually replacing 'belief' with evidence, this represents a case study in resolving environmental disputes.     

New journal: Algorithms for Molecular Biology

This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computatioal biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed Central and other scientific archives. We are looking forward to receiving your contributions.     

Using caching and optimization techniques to improve performance of the Ensembl website

Background  

The Ensembl web site has provided access to genomic information for almost 10 years. During this time the amount of data available through Ensembl has grown dramatically. At the same time, the World Wide Web itself has become a dramatically more important component of the scientific workflow and the way that scientists share and access data and scientific information.     

Bamboo-infoline: A database for North Bengal Bamboo's

Bamboo, the "Green Gold", included in the non-timber forest products has both ecological and economic importance. Here is an attempt to describe a database named "Bambooinfoline" , which provides enumeration of the different species of bamboos found in North Bengal, with special emphasis on taxonomy, edible properties, chemical constituents, morphological features along with tissue culture specifications, which in turn benefits of scientific community. AVAILABILITY: The database is freely available at http://www.bamboodb.ind.in/     

The Importance of Biodiversity E-infrastructures for Megadiverse Countries

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil’s speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2–4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish.     

Open Access, Open Systems: Pastoral Management of Common-Pool Resources in the Chad Basin

The discussion about the impact of pastoralists on ecosystems has been profoundly shaped by Hardin’s tragedy of the commons that held pastoralists responsible for overgrazing the range. Research has shown that grazing ecosystems are much more complex and dynamic than was previously assumed and that they can be managed adaptively as commons. However, proponents and critics of Hardin’s thesis continue to argue that open access to common-pool resources inevitably leads to a tragedy of the commons. A longitudinal study that we conducted of pastoral mobility and primary production in the Logone floodplain in the Far North Region of Cameroon suggest that open access does not have to lead to a tragedy of the commons. We argue that this pastoral system is best conceptualized as an open system, in which a combination of individual decision-making and coordination of movements leads to an ideal-free type of distribution of mobile pastoralists. We explain how this self-organizing system of open access works and its implications for theories of management of common-pool resources and our understanding of pastoral systems.     

Open access radiology services: availability to general practitioners in the UK.

A postal survey was carried out among secretaries of local medical committees to ascertain the availability of open access to radiology services in the United Kingdom. The results from different areas showed a wide variation of access, ranging from virtually none to complete access. General practitioner representatives on management teams might encourage open access to radiology services, and health authorities might be encouraged to introduce complete open access.     

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accepting data submissions from all over the world, and providing free open access to all publicly available data in support of worldwide research activities.     

Virtual Reality: Beyond Visualization

Virtual reality (VR) has recently become an affordable technology. A wide range of options are available to access this unique visualization medium, from simple cardboard inserts for smartphones to truly advanced headsets tracked by external sensors. While it is now possible for any research team to gain access to VR, we can still question what it brings to scientific research. Visualization and the ability to navigate complex three-dimensional data are undoubtedly a gateway to many scientific applications; however, we are convinced that data treatment and numerical simulations, especially those mixing interactions with data, human cognition, and automated algorithms will be the future of VR in scientific research. Moreover, VR might soon merit the same level of attention to imaging data as machine learning currently has. In this short perspective, we discuss approaches that employ VR in scientific research based on some concrete examples.     

Open by default: a proposed copyright license and waiver agreement for open access research and data in peer-reviewed journals

ABSTRACT: Copyright and licensing of scientific data, internationally, are complex and present legal barriers to data sharing, integration and reuse, and therefore restrict the most efficient transfer and discovery of scientific knowledge. Much data are included within scientific journal articles, their published tables, additional files (supplementary material) and reference lists. However, these data are usually published under licenses which are not appropriate for data. Creative Commons CC0 is an appropriate and increasingly accepted method for dedicating data to the public domain, to enable data reuse with the minimum of restrictions. BioMed Central is committed to working towards implementation of open data-compliant licensing in its publications. Here we detail a protocol for implementing a combined Creative Commons Attribution license (for copyrightable material) and Creative Commons CC0 waiver (for data) agreement for content published in peer-reviewed open access journals. We explain the differences between legal requirements for attribution in copyright, and cultural requirements in scholarship for giving individuals credit for their work through citation. We argue that publishing data in scientific journals under CC0 will have numerous benefits for individuals and society, and yet will have minimal implications for authors and minimal impact on current publishing and research workflows. We provide practical examples and definitions of data types, such as XML and tabular data, and specific secondary use cases for published data, including text mining, reproducible research, and open bibliography. We believe this proposed change to the current copyright and licensing structure in science publishing will help clarify what users -- people and machines -- of the published literature can do, legally, with journal articles and make research using the published literature more efficient. We further believe this model could be adopted across multiple publishers, and invite comment on this article from all stakeholders in scientific research.     

Bibliometric indicators realities, myth and prospective

The impact factor of scientific reviews, calculated by the Institute for Scientific Information (ISI), is increasingly used to evaluate the performance of scientists and programmes. Bibliometric indicators, originally designed for other purposes than individual evaluation, are very useful tools provided their interpretation is not extrapolated beyond their limits of validity. Here we present a critical analysis of appropriate uses and misuses of bibliometric data based on case studies. We also outline anticipated consequences of new information technologies, such as electronic journals or open access schemes, on the mode of science production, evaluation and dissemination in biomedical sciences.     

Patenting nonassociated polymeric structures (NAPS): implications for structural genomic data release

The intellectual property laws that govern patent rights should provide a reasonable balance between the competing concerns of open access and exclusivity. Open access can facilitate knowledge dissemination and collaboration in furthering science. On the other hand, exclusivity can ensure interest and financial investment in scientific research and development.In recent days, the appropriate balance between open access and exclusivity has been a focus of public debate, particularly with regard to genomic inventions and their applications. In seeking to reconcile the timing of structural genomic data release with certain efforts to secure intellectual property rights, the International Structural Genomics Organisation joins others confronting this controversy.This paper seeks to inform the discussion with an overview of the U.S. standards for patenting nonassociated polymeric structures (NAPS), which include polynucleotides or polypeptides of unknown biological significance, and their corresponding structural data. In the United States, the present ability to obtain patent rights to these discoveries appears problematic given the requirement of specific, substantial and credible utility, among other things. Without demonstrable utility, NAPS and NAPS-related data likely will not be entitled to patent protection, whether the U.S. Patent & Trademark Office rejects NAPS claims as unpatentable in the first instance, or the U.S. federal courts invalidate NAPS claims in later patent litigation. As such, the improbability of obtaining enforceable patent rights to NAPS might undermine the rationale for delaying structural genomic data release to allow for the filing of patent applications in this regard.Abbreviations: ESTs, expressed sequence tags; ISGO, International Structural Genomics Organisation; NAPS, nonassociated polymeric structures; SNPs, single nucleotide polymorphisms; USPTO, U.S. Patent & Trademark Office     

Citizen science and wildlife biology: Synergies and challenges

Citizen science (CS) has evolved over the past decades as a working method involving interested citizens in scientific research, for example by reporting observations, taking measurements or analysing data. In the past, research on animal behaviour has been benefitting from contributions of citizen scientists mainly in the field of ornithology but the full potential of CS in ecological and behavioural sciences is surely still untapped. Here, we present case studies that successfully applied CS to research projects in wildlife biology and discuss potentials and challenges experienced. Our case studies cover a broad range of opportunities: large‐scale CS projects with interactive online tools on bird song dialects, engagement of stakeholders as citizen scientists to reduce human–wildlife conflicts, involvement of students of primary and secondary schools in CS projects as well as collaboration with the media leading to successful recruitment of citizen scientists. Each case study provides a short overview of the scientific questions and how they were approached to showcase the potentials and challenges of CS in wildlife biology. Based on the experience of the case studies, we highlight how CS may support research in wildlife biology and emphasise the value of fostering communication in CS to improve recruitment of participants and to facilitate learning and mutual trust among different groups of interest (e.g., researchers, stakeholders, students). We further show how specific training for the participants may be needed to obtain reliable data. We consider CS as a suitable tool to enhance research in wildlife biology through the application of open science procedures (i.e., open access to articles and the data on publicly available repositories) to support transparency and sharing experiences.     

Integration of open access literature into the RCSB Protein Data Bank using BioLit

Background  

Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright restriction, this distinction between database and literature is blurring. To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB).