Monitoring Bulletin – September 2020
- What’s new in your disciplines
- Debate about scientific integrity
- Storage, data warehouses and electronic lab notebooks
What’s new in your disciplines
Several million euros for chemical data management in Germany. The German government is providing €90 million over the next 5 years to improve data-research management. Of the 30 bodies selected, two are specialized in chemistry (NFDI4Chem and NFDICat), beneficiaries indicated in a webinar at the end of July. Each body will receive approximately €2.3 million. Priorities include improving the international visibility of chemistry data warehouses, establishing a basic chemistry-specific standards for data description, making metadata readable, and promoting the use of electronic laboratory notebooks. A 5-year project to develop the Chemotion solution (open source e-book) is planned.
ACS launches new open access journals. The publisher annonces the publication, planned for January 2021, of Jacs Au (pronounced “Jacs Gold”, referring to the author-payer model). All issues will be open access, unlike Jacs, which remains a hybrid magazine (paid subscription and publication of articles with open access on request with publication fees). ACS also indicates that the other difference between Jacs Au and Jacs is the composition of the publication board. At the same time, ACS will launch nine other open-access scientific journals.
ACS magazines: two new publications about agriculture and food. ACS Agricultural Science Technology and ACS Food Science & Technology will focus on the latest scientific and technological innovations in agriculture research and food and nutrition science, the publisher explains. The first issues will be released in January 2021.
In Grenoble, Synchrotron ESRF-EBS reopened on August 25 after 20 months of work. The first 4th-generation high-energy synchrotron is now available to researchers and their research-data policy is available for consultation.
APS launches a new open-access quantum physics journal. The first issue PRX Quantum has just been released. Open access and an extension of the new journal Physical Review X (or PRX), PRX Quantum plans to cover the latest scientific developments in quantum information.
Nearly 200 open-access reviews have disappeared. This was the conclusion of preprint posted on ArXiv at the end of August. Between 2000 and 2019, 176 scientific journals covering all disciplines, only available on-line, are no longer accessible due to insufficient maintenance and storage policies. Humanities are the most effected. Of the 52 journals in Europe, only 3 are about life sciences and 8 about physics and mathematics.
Portrait of a chemist. UCBL looked into the common center for mass spectrometry, where Elodie Fromentin is research engineer at ICBMS. In this interview, she tells us about the role of the platform for researchers and private companies, and explains how lockdown has advanced the development of digital practices.
A debate about scientific integrity
Fake chemistry data. An article in the German magazine “Angewandte Chemie International Edition” was withdrawn due to false data. The authors, Alessandro Passera and Antonio Mezzetti admitted data in the article had been manipulated.
Chemistry and artificial intelligence. The August 2020 issue of the Journal of Medicinal Chemistry focused on the use of machine learning in pharmaceutical research. The subject is echoed in an article published on September 15 in the “Angewandte Chemie International Edition”. The potential of algorithms – deemed immense – depends on the availability of reliable data. The author explains, “High-quality data is scarce, particularly in the field of synthetic chemistry, and datasets are often dependent on human bias, or quite simply not available.”
Negative results: researchers recognize the benefits, but don’t have time. According to a study conducted with a scientific network about the ARN, 82% of researchers consider that negative results should be shared. On the other hand, only 14% try to do so. For over half of researchers, not sharing is due to lack of time. A negative result is “any result that does not confirm a hypothesis or does not permit the reproduction of previously published data.” By contrast, the publication of so-called “positive” results has soared over the years, according to authors of the study. A conflicting observation resulting partly from increasing “scientific misconduct” and “insufficient reproducibility of results.”
Reproducibility in physics. Gaël Mourouga, PhD student in physics at the specialized Zurich university (ZHAW), explains the difficulties encountered during his PhD thesis (see video below). This is the latest data story published on the site. All the interviews of PhD students and researchers are available here. The subject of reproducibility is also discussed in Passport to Open Science, published in September for PhD students.
Reproducibility in chemistry: preserving computer code. “Even in the same lab, the work of one student can not be used by another, due to insufficient records,” explains Konrad Hinsen, in the columns of Chemistry world. Researcher at the Center for Molecular Biophysics (CBM) in Orléans, he recently launched a challenge to his peers: run a program from code written ten years ago. Progressive code sharing on GitHub or Zenodo can help to ensure use and updates. Another initiative by eLife journal, covering life sciences, now offers authors the ERA (Executable Research Article) option, where code and text can be mixed (via Python or Markdown). See the example (click on ‘Run document’).
Reinforce OFIS skills. In a report published this summer, the parliamentary office for the evaluation of scientific and technological choices addresses scientific integrity in France. Elected representatives hope to massively increase the prerogatives of the OFIS by changing its status to an independent administrative authority. There is also a plan to include scientific integrity training for PhD students or any new people authorized to conduct research. These proposals are in line with a report published early in September by a collective of researchers and medical professionals, who listed “abnormal” practices by a “minority” who benefit from a feeling of “impunity”. The topic is also central to “Hong Kong principles” presented at the 6th world conference on scientific integrity where the 3rd subject focused on data sharing.
Bill for multi-year research programs. This controversial text was voted by the National Assembly at the first presentation on September 23. In a supporting document, 39 academic societies, including the French chemical and physics societies proposed 24 amendments. Issues included “insufficient reference to scientific integrity” and the need for “OFIS to establish a public list of predatory scientific journals in order to prevent their dubious content from being published in the media.”
Predator journals: a critical issue. In a preprint made available in HAL, Chéifa Boukacem-Zeghmouri, Sarah Rakotoary and Pascal Bador, from the Elico research team, report on the issue of predatory journals, estimated to reach 13,000 in number. As well as the absence of peer-review, false impact factors and pushover editorial committees, the article also indicates the creation of black lists that distinguish between approved and banned journals. But they are not free!
An on-line course about research ethics. Université de Lyon opens the 5th session of its MOOC about research ethics. The 5-week on-line course features interviews with researchers about a range of issues. Registrations open until October 20. The MOOC is complementary with the MOOC about scientific integrity by University of Bordeaux proposed on FUN-MOOC.
Storage, data warehouses and electronic lab notebooks
To share or not to share – that is the question. A study published in the journal Plos lists several factors identified in scientific literature that may influence researchers to share their data. Academic staff, busy with course preparation and research, are less likely to share data than researchers that do not teach. Similarly, untenured researchers are less likely to share their experimental data than staff with tenure. Finally, older researchers are more willing to publish their data than younger researchers.
Data warehouses: disagreement about partners. The decision by the Dutch 4TU warehouse to abandon the open-source Fedora solution and use the Figshare infrastructure (backed by Digital Science, acquired by the editorial group Holtzbrinck, which also owns Springer Nature) raises many questions. According to 4TU administrators, the public call for bids did not attract candidates from open source solutions. In their joint response, Zenodo and Dryad, both backed by open-source infrastructures, offer a different perspective: the public call for bids generates “bureaucracy” that “eliminated us from competition”.
LabCollector unveils a new version of their electronic laboratory workbook. The 6th version of the LabCollector e-book has a new responsive interface design, improved user management and new capacity for interfacing with laboratory instruments. More details here.
An open-science specialist at Lyon 1. Chérifa Boukacem Zegmouri, IT academic, has been named as open-science specialist at UCBL. This is the first nomination to the role. She will propose “guidelines and actions” to university governance in accordance with the national and European open-science framework.
A research-data administrator at MESRI. Isabelle Blanc will start as research-data administrator for the Ministry of Research and Higher Education on November 1. She has held the same position at INRAE.
A French man at the head of the ERC. After a first term from 2014 to 2019, mathematician Jean-Pierre Bourguignon was named acting chairman of the organization. The decision follows the resignation of Italian Mauro Ferrari last April.
Rencontre avec les chercheurs en physique sur l’enjeu des données. Le 18 septembre, une rencontre sur la gestion des données, organisée par les laboratoires LPMMC, LNCMI et l’Institut Neel à Grenoble, a abouti au lancement d’un partenariat entre le projet Datacc, la cellule Data Stewardship de l’UGA et plusieurs projets de recherche afin de pouvoir accompagner les chercheurs dans leurs pratiques courantes en matière de gestion des données.
“Prendre soin de ses données.” C’est le thème de la journée qu’organise de l’Université de Lorraine le 8 octobre prochain. Cette manifestation aura lieu uniquement en ligne. Inscription gratuite, programme et détails de connexion sur le site de l’événement.
“Rendre FAIR les données, mais quelles données préserver ?” : la vidéo est en ligne ! L’atelier Dialog’IST du 9 juillet dernier a ouvert les débats sur plusieurs questions importantes : “Que faut-il préserver et que peut-on éliminer ? Quel est le cadre juridique qui sous-tend ces problématiques ? Quelles conditions techniques jouent un rôle et sont à prendre en considération ?”. Au travers de plusieurs retours d’expérience, l’atelier a permis de croiser le regard de différents métiers (chercheurs, archivistes, bibliothécaires).
“A qui appartiennent les données ?” C’est à cette épineuse question que répondait Lionel Maurel, juriste et bibliothécaire, directeur adjoint scientifique de l’InSHS lors d’un webinaire organisé par le réseau Mate-SHS le 14 septembre. Les supports de présentation ainsi que l’enregistrement du webinaire sont disponibles.