Opening the Publication Process with Executable Research Compendia

Authors : Daniel Nüst, Markus Konkol, Marc Schutzeichel, Edzer Pebesma, Christian Kray, Holger Przibytzin, Jörg Lorenz

A strong movement towards openness has seized science. Open data and methods, open source software, Open Access, open reviews, and open research platforms provide the legal and technical solutions to new forms of research and publishing.

However, publishing reproducible research is still not common practice. Reasons include a lack of incentives and a missing standardized infrastructure for providing research material such as data sets and source code together with a scientific paper. Therefore we first study fundamentals and existing approaches.

On that basis, our key contributions are the identification of core requirements of authors, readers, publishers, curators, as well as preservationists and the subsequent description of an executable research compendium (ERC). It is the main component of a publication process providing a new way to publish and access computational research.

ERCs provide a new standardisable packaging mechanism which combines data, software, text, and a user interface description. We discuss the potential of ERCs and their challenges in the context of user requirements and the established publication processes.

We conclude that ERCs provide a novel potential to find, explore, reuse, and archive computer-based research.


Research Data Reusability: Conceptual Foundations, Barriers and Enabling Technologies

Author : Costantino Thanos

High-throughput scientific instruments are generating massive amounts of data. Today, one of the main challenges faced by researchers is to make the best use of the world’s growing wealth of data. Data (re)usability is becoming a distinct characteristic of modern scientific practice.

By data (re)usability, we mean the ease of using data for legitimate scientific research by one or more communities of research (consumer communities) that is produced by other communities of research (producer communities).

Data (re)usability allows the reanalysis of evidence, reproduction and verification of results, minimizing duplication of effort, and building on the work of others. It has four main dimensions: policy, legal, economic and technological. The paper addresses the technological dimension of data reusability.

The conceptual foundations of data reuse as well as the barriers that hamper data reuse are presented and discussed. The data publication process is proposed as a bridge between the data author and user and the relevant technologies enabling this process are presented.

URL : Research Data Reusability: Conceptual Foundations, Barriers and Enabling Technologies


Améliorer l’exposition des données de la recherche : la publication de data papers

Auteur/Author : Nathalie Reymonet

Les données de la recherche sont l’objet de l’intérêt des financeurs de la recherche publique, qui incitent les chercheurs à partager ces données, afin de répondre à des enjeux financiers comme de circulation des savoirs.

Parmi les différentes modalités de la communication scientifique, la publication d’un « data paper » est une démarche relativement nouvelle. Le « data paper », ou article sur des données, décrit des données scientifiques et propose un lien vers un entrepôt de données qui les stocke.

La description est en particulier très précise sur les points techniques et la méthodologie de production des données. Cette démarche va dans le sens de l’exposition des données, de leur accessibilité, leur interopérabilité et leur réutilisabilité, répondant ainsi aux recommandations des communautés d’intérêt de la recherche académique.

Ce texte présente la structure et le contenu d’un « data paper » ainsi que des exemples de revues qui publient de tels articles.

URL : Améliorer l’exposition des données de la recherche : la publication de data papers

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Knowledge Sharing as a Social Dilemma in Pharmaceutical Innovation

Author : Daria Kim

The article addresses the problem of restricted access to industry-sponsored clinical trial data. In particular, it analyses the intersection of the competing claims that mandatory disclosure of pharmaceutical test data impedes innovation incentives, and that access facilitates new drug development.

These claims are characterised in terms of public-good and common-resource dilemmas. The analysis finds that confidentiality protection of primary research data plays an ambiguous role.

While secrecy, as such, does not solve the public-good problem in pharmaceutical innovation (in the presence of regulatory instruments that protect the originator drug against generic competition), it is likely to exacerbate the common-resource problem, in view of data as a source of verified and new knowledge.

It is argued that the claim of the research-based industry that disclosure of clinical data impedes innovation incentives is misplaced and should not be leveraged against the pro-access policies. The analysis proposes that regulation should adhere to the principle that protection should be confined to competition by imitation.

This implies that the rules of access should be designed in such a way that third-party use of data does not interfere with protection against generic competition. At the same time, the long-term collective benefit can be maximised when the ‘cooperative choice’ – i.e. when everyone shares data – becomes the ‘dominant strategy’.

This can be achieved only when access is not subject to the authorisation of the initial trial sponsors, and when primary data is aggregated, refined and managed on the collective basis.


A l’épreuve de l’hétérogénéité : données de recherche et interdisciplinarité : L’exemple du projet européen IPERION-CH

Auteur/Author : Marie Puren

Avec la mise en place de grandes infrastructures de recherche en sciences du patrimoine comme E-RIHS, on rassemble des acteurs divers, issus à la fois des sciences humaines et sociales et des sciences expérimentales. Le paléontologue croise l’historien de l’art, et le physicien collabore avec le restaurateur.

Dans ce cadre, la gestion des données de la recherche est un véritable défi, car elle doit rassembler, valoriser et rendre accessibles des données produites par des protagonistes très différents, utilisant des méthodes elles aussi très différentes. Comment en effet gérer et échanger à la fois des données d’expériences, des images numérisées et des rapports de restauration ?

Le cycle de vie des données de la recherche, de leur création à leur diffusion en passant par leur analyse, au sein de cette communauté interdisciplinaire interroge la définition même de ce type de données, et nous amène à questionner les pratiques autour de celles-ci.


Open supply? On the future of document supply in the world of open science

Author : Joachim Schöpfel


The purpose of this paper is to propose a personal viewpoint on the development of document supply in the context of the recent European Union (EU) decisions on open science.


The paper provides some elements to the usual questions of service development, about business, customers, added value, environment and objectives.


The EU goal for open science is 100 per cent available research results in 2020. To meet the challenge, document supply must change, include more and other content, serve different targets groups, apply innovative technology and provide knowledge. If not, document supply will become a marginalized library service.


Basically, open science is not library-friendly, and it does not offer a solution for the actual problems of document supply. But it may provide an opportunity for document supply to become a modern service able to deal with new forms of unequal access and digital divide.


Towards an open science publishing platform

Authors : Vitek Tracz, Rebecca Lawrence

The way science and research is done is rapidly becoming more open and collaborative. The traditional way of publishing new findings in journals is becoming increasingly outdated and no longer serves the needs of much of science.

Whilst preprints can bring significant benefits of removing delay and selection, they do not go far enough if simply implemented alongside the existing journal system. We propose that we need a new approach, an Open Science Platform, that takes the benefits of preprints but adds formal, invited, and transparent post-publication peer review.

This bypasses the problems of the current journal system and, in doing so, moves the evaluation of research and researchers away from the journal-based Impact Factor and towards a fairer system of article-based qualitative and quantitative indicators.

In the long term, it should be irrelevant where a researcher publishes their findings. What is important is that research is shared and made available without delay within a framework that encourages quality standards and requires all players in the research community to work as collaborators.

URL : Towards an open science publishing platform