Low availability of code in ecology: A call for urgent action

Authors : Antica Culina, Ilona van den Berg, Simon Evans, Alfredo Sánchez-Tójar

Access to analytical code is essential for transparent and reproducible research. We review the state of code availability in ecology using a random sample of 346 nonmolecular articles published between 2015 and 2019 under mandatory or encouraged code-sharing policies.

Our results call for urgent action to increase code availability: only 27% of eligible articles were accompanied by code. In contrast, data were available for 79% of eligible articles, highlighting that code availability is an important limiting factor for computational reproducibility in ecology.

Although the percentage of ecological journals with mandatory or encouraged code-sharing policies has increased considerably, from 15% in 2015 to 75% in 2020, our results show that code-sharing policies are not adhered to by most authors.

We hope these results will encourage journals, institutions, funding agencies, and researchers to address this alarming situation.

URL : Low availability of code in ecology: A call for urgent action

DOI : https://doi.org/10.1371/journal.pbio.3000763

Le principe d’ouverture des données de la recherche scientifique. Réflexions autour du croisement de l’informatique et du droit

Auteur/Author : Agnès Robin

Les données de la recherche scientifique sont actuellement soumises à un programme de standardisation technique (FAIR) dont l’objectif est d’en permettre la diffusion aux fins de réutilisation par le public (entreprises privées ou autre).

Cette politique, qui sans se confondre avec elle, converge avec celle dite de « science ouverte », s’articule autour d’un principe normatif conflictuel, selon lequel le résultats de la recherche (et donc les données) doivent être « aussi ouverts que possibles et pas plus fermés que nécessaire », obligeant alors les chercheurs, ingénieurs et documentalistes, éventuellement chargés de la gestion des données de la recherche, à procéder à une qualification juridique délicate des données.

URL : http://intelligibilite-numerique.numerev.com/index.php/numeros/n-1-2020/9-le-principe-d-ouverture-des-donnees-de-la-recherche-scientifique

Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications

Authors : Antonia Lock, Midori A Harris, Kim Rutherford, Jacqueline Hayles, Valerie Wood

Maximizing the impact and value of scientific research requires efficient knowledge distribution, which increasingly depends on the integration of standardized published data into online databases.

To make data integration more comprehensive and efficient for fission yeast research, PomBase has pioneered a community curation effort that engages publication authors directly in FAIR-sharing of data representing detailed biological knowledge from hypothesis-driven experiments.

Canto, an intuitive online curation tool that enables biologists to describe their detailed functional data using shared ontologies, forms the core of PomBase’s system.

With 8 years’ experience, and as the author response rate reaches 50%, we review community curation progress and the insights we have gained from the project.

We highlight incentives and nudges we deploy to maximize participation, and summarize project outcomes, which include increased knowledge integration and dissemination as well as the unanticipated added value arising from co-curation by publication authors and professional curators.

URL : Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications

DOI : https://doi.org/10.1093/database/baaa028

FAIR Digital Objects for Science: From Data Pieces to Actionable Knowledge Units

Authors : Koenraad De Smedt, Dimitris Koureas, Peter Wittenburg

Data science is facing the following major challenges: (1) developing scalable cross-disciplinary capabilities, (2) dealing with the increasing data volumes and their inherent complexity, (3) building tools that help to build trust, (4) creating mechanisms to efficiently operate in the domain of scientific assertions, (5) turning data into actionable knowledge units and (6) promoting data interoperability.

As a way to overcome these challenges, we further develop the proposals by early Internet pioneers for Digital Objects as encapsulations of data and metadata made accessible by persistent identifiers.

In the past decade, this concept was revisited by various groups within the Research Data Alliance and put in the context of the FAIR Guiding Principles for findable, accessible, interoperable and reusable data.

The basic components of a FAIR Digital Object (FDO) as a self-contained, typed, machine-actionable data package are explained. A survey of use cases has indicated the growing interest of research communities in FDO solutions.

We conclude that the FDO concept has the potential to act as the interoperable federative core of a hyperinfrastructure initiative such as the European Open Science Cloud (EOSC).

URL : FAIR Digital Objects for Science: From Data Pieces to Actionable Knowledge Units

Alternative location : https://www.mdpi.com/2304-6775/8/2/21

Digital Objects – FAIR Digital Objects: Which Services Are Required?

Author : Ulrich Schwardmann

Some of the early Research Data Alliance working groups reused the notion of digital objects as digital entities described by metadata and referenced by a persistent identifier. In recent times the FAIR principles became a prominent role as framework for the sustainability of scientific data.

Both approaches had always machine actionability, the capability of computational systems to use services on data without human intervention, in their focus. The more technical approach of digital objects turned out to provide a complementary view on several aspects of the policy framework of FAIR from a technical perspective.

After a deeper analysis and integration of these concepts by a group of European data experts the discussion intensified on so called FAIR digital objects. But they need to be accompanied by services as building blocks for automated processes. We will describe the components of this framework and its potentials here, and also which services inside this framework are required.

URL : Digital Objects – FAIR Digital Objects: Which Services Are Required?

DOI : http://doi.org/10.5334/dsj-2020-015

The Heritage Data Reuse Charter: from principles to research workflows

Authors : Erzsébet Tóth-Czifra, Laurent Romary

There is a growing need to establish domain-or discipline-specific approaches to research data sharing workflows. A defining feature of data and data workflows in the arts and humanities domain is their dependence on cultural heritage sources hosted and curated in museums, libraries, galleries and archives.

A major difficulty when scholars interact with heritage data is that the nature of the cooperation between researchers and Cultural Heritage Institutions (henceforth CHIs) is often constrained by structural and legal challenges but even more by uncertainties as to the expectations of both parties.

The Heritage Data Reuse Charter aims to address these by designing a common environment that will enable all the relevant actors to work together to connect and improve access to heritage data and make transactions related to the scholarly use of cultural heritage data more visible and transparent.

As a first step, a wide range of stakeholders on the Cultural Heritage and research sector agreed upon a set of generic principles, summarized in the Mission Statement of the Charter, that can serve as a baseline governing the interactions between CHIs, researchers and data centres.

This was followed by a long and thorough validation process related to these principles through surveys 1 and workshops 2. As a second step, we now put forward a questionnaire template tool that helps researchers and CHIs to translate the 6 core principles into specific research project settings.

It contains questions about access to data, provenance information, preferred citation standards, hosting responsibilities etc. on the basis of which the parties can arrive at mutual reuse agreements that could serve as a starting point for a FAIR-by-construction data management, right from the project planning/application phase.

The questionnaire template and the resulting mutual agreements can be flexibly applied to projects of different scale and in platform-independent ways. Institutions can embed them into their own exchange protocols while researchers can add them to their Data Management Plans.

As such, they can show evidence for responsible and fair conduct of cultural heritage data, and fair (but also FAIR) research data management practices that are based on partnership with the holding institution.

URL : https://halshs.archives-ouvertes.fr/halshs-02475692