The Dawn of Open Access to Phylogenetic Data

« The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation – extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Importantly, our survey spans recent policy initiatives and infrastructural changes; our analyses indicate that the positive impact of these community initiatives has been both dramatic and immediate. Although the results of our study indicate that the situation is dire, our findings also reveal tremendous recent progress in the sharing and preservation of phylogenetic data. »

URL : The Dawn of Open Access to Phylogenetic Data

DOI: 10.1371/journal.pone.0110268

Open exchange of scientific knowledge and European copyright: The case of biodiversity information

« Background. The 7th Framework Programme for Research and Technological Development is helping the European to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme “Horizon 2020” aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights.

We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information.

Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation. »

URL : Open exchange of scientific knowledge and European copyright

Alternative URL :

Ten Simple Rules for the Care and Feeding of Scientific Data

« This article offers a short guide to the steps scientists can take to ensure that their data and associated analyses continue to be of value and to be recognized. In just the past few years, hundreds of scholarly papers and reports have been written on questions of data sharing, data provenance, research reproducibility, licensing, attribution, privacy, and more—but our goal here is not to review that literature. Instead, we present a short guide intended for researchers who want to know why it is important to “care for and feed” data, with some practical advice on how to do that. The final section at the close of this work offers links to the types of services referred to throughout the text. »

URL : Ten Simple Rules for the Care and Feeding of Scientific Data

Alternative URL :

GigaDB promoting data dissemination and reproducibility Often…

GigaDB: promoting data dissemination and reproducibility :

« Often papers are published where the underlying data supporting the research are not made available because of the limitations of making such large data sets publicly and permanently accessible. Even if the raw data are deposited in public archives, the essential analysis intermediaries, scripts or software are frequently not made available, meaning the science is not reproducible. The GigaScience journal is attempting to address this issue with the associated data storage and dissemination portal, the GigaScience database (GigaDB). Here we present the current version of GigaDB and reveal plans for the next generation of improvements. However, most importantly, we are soliciting responses from you, the users, to ensure that future developments are focused on the data storage and dissemination issues that still need resolving. »


De l’Open data à l’Open research data : quelle(s) politique(s) pour les données de recherche?

Le mouvement du libre-accès aux publications scientifiques s’élargit de plus en plus aux données de la recherche. Des initiatives pour garantir l’accessibilité et la complète réutilisation de ces données sont prises par une grande diversité d’acteurs – États, agences de financement de la recherche, éditeurs, communautés scientifiques.

L’ouverture des données de la recherche est rendue possible par la définition de politiques incitatives ou contraignantes, l’adoption de solutions juridiques et techniques, mais repose avant tout sur de bonnes pratiques de gestion des données. Tandis que la France s’insère progressivement dans la dynamique de l’Open research data, les universités sont appelées à définir leur politique de données.

Les bibliothécaires ont un rôle majeur à jouer dans l’élaboration de ces politiques, peuvent contribuer à identifier les besoins des chercheurs et les assister sur le volet « métadonnées ». Aussi, la question de l’ouverture des données de recherche offre une opportunité unique à ces professionnels de la documentation : celle de remodeler, à l’échelle des établissements de recherche, leur(s) lien(s) avec la communauté des chercheurs. »

URL : De l’Open Data à l’Open research data

URL alternative :

Growing Institutional Support for Data Citation Results of…

Growing Institutional Support for Data Citation : Results of a Partnership Between Griffith University and the Australian National Data Service :

« Data is increasingly recognised as a valuable product of research and a number of international initiatives are underway to ensure it is better managed, connected, published, discovered, cited and reused. Within this context, data citation is an emergent practice rather than a norm of scholarly attribution. In 2012, a data citation project at Griffith University funded by the Australian National Data Service (ANDS) commenced that aimed to: enhance existing infrastructure for data citation at the University; test methodologies for tracking impact; and provide targeted outreach to researchers about the benefits of data citation. The project extended previous collaboration between Griffith and ANDS that built infrastructure at the University to assign DOI names (Digital Object Identifiers) to research data produced by Griffith’s researchers. This article reports on the findings of the project and provides a case study of what can be achieved at the institutional level to support data citation. »


Data sharing and its implications for academic libraries…

Data sharing and its implications for academic libraries :

« Purpose : As an important aspect of the scientific process, research data sharing is the practice of making data used for scholarly research publicly available for use by other researchers. This paper seeks to provide a more comprehensive understanding of the data-sharing challenges and opportunities posed by the data deluge in academics. An attempt is made to discuss implications for the changing role and functioning of academic libraries.

Design/methodology/approach : An extensive review of literature on current trends and the impact of data sharing are performed.

Findings : The context in which the increasing demands for data sharing have arisen is presented. Some of the practices, trends, and issues central to data sharing among academics are presented. Emerging implications for academic libraries that are expected to provide a data service are discussed.

Originality/value : An insightful review and synthesis of context, issues, and trends in data sharing will help academic libraries to plan and develop programs and policies for their data services. »