Biodiversity Literature Repository: Building the customized FAIR repository by using custom metadata

In the landscape of general-purpose repositories, Zenodo was built at the European Laboratory for Particle Physics' (CERN) data center to facilitate the sharing and preservation of the long tail of research across all disciplines and scientific domains. Given Zenodo’s long tradition of making research artifacts FAIR (Findable, Accessible, Interoperable, and Reusable), there are still challenges in applying these principles effectively when serving the needs of specific research domains. Plazi’s biodiversity taxonomic literature processing pipeline liberates data from publications, making it FAIR via extensive metadata, the minting of a DataCite Digital Object Identifier (DOI), a licence and both human- and machine-readable output provided by Zenodo, and accessible via the Biodiversity Literature Repository community at Zenodo. The deposits (e.g., taxonomic treatments, figures) are an example of how local networks of information can be formally linked to explicit resources in a broader context of other platforms like GBIF (Global Biodiversity Information Facility). In the context of biodiversity taxonomic literature data workflows, a general-purpose repository’s traditional submission approach is not enough to preserve rich metadata and to capture highly interlinked objects, such as taxonomic treatments and digital specimens. As a prerequisite to serve these use cases and ensure that the artifacts remain FAIR, Zenodo introduced the concept of custom metadata, which allows enhancing submissions such as figures or taxonomic treatments (see as an example the treatment of Eurygyrus peloponnesius) with custom keywords, based on terms from common biodiversity vocabularies like Darwin Core and Audubon Core and with an explicit link to the respective vocabulary term. The aforementioned pipelines and features are designed to be served first and foremost using public Representational State Transfer Application Programming Interfaces (REST APIs) and open web technologies like webhooks. This approach allows researchers and platforms to integrate existing and new automated workflows into Zenodo and thus empowers research communities to create self-sustained cross-platform ecosystems. The BiCIKL project (Biodiversity Community Integrated Knowledge Library) exemplifies how repositories and tools can become building blocks for broader adoption of the FAIR principles. Starting with the above literature processing pipeline, the concepts of and resulting FAIR data, with a focus on the custom metadata used to enhance the deposits, will be explained.

Industry careers for molecular bioscientists: an interview with Jennifer Mitchell

Jennifer Mitchell is a scientist at Redx Pharma and Board Member of the European Laboratory Research and Innovation Group (ELRIG). She completed her integrated undergraduate and master’s degree in biological sciences at the University of Liverpool and took on a graduate industrial role as an associate scientist at a biotech company. After 2 years in this role, she went back into academia to complete a PhD before moving back to industry. Jennifer began her involvement with ELRIG, a not-for-profit organization serving the life science and drug discovery communities, as a student volunteer in 2017 and she has been part of the ELRIG General Committee since 2018. She is also part of the ELRIG early career professional (ECP) workgroup, which aims to engage the ECP scientific community through career development workshops and outreach events. In December 2020, the Biochemical Society hosted a session on industry careers in the molecular biosciences as part of its Biochemistry Focuswebinar series dedicated to early career researchers. The Biochemist spoke to Jennifer, panellist on the day, to find out more about her experience working in industry and her broader contributions to the community.

COMBACTE LAB-Net: building a European laboratory network for clinical trials on anti-infectives

LAB-Net, the laboratory network of COMBACTE, has established itself as an indispensable network for clinical trials in infectious diseases that plays a crucial part across 30 clinical studies not only within, but also outside the COMBACTE consortium. Since its official launch in January 2013, LAB-Net has expanded more than threefold and in Q4 2020 it encompasses 841 labs across 41 countries in Europe. In addition, LAB-Net has crossed the European borders and collaborates with more than 300 laboratories spread across the globe. The tight collaboration with partners within COMBACTE and beyond contributed tremendously to the growth of LAB-Net over the years. A sustainable infrastructure beyond COMBACTE-NET is needed to ensure the smooth handover and continuity of the achievements made by the project.

Melanie Leveridge on ELRIG and a career in drug discovery

Melanie Leveridge is a Senior Director at GSK, a science-led global healthcare company headquartered in Brentford, UK. She has recently been elected Chair of ELRIG (York, UK), the European Laboratory Research and Innovation Group. Here she speaks to Future Drug Discovery Editor Jennifer Straiton about what she hopes to achieve during her tenure as ELRIG Chair and gives her advice for Early Career Researchers just starting out in the field of drug discovery.

Design of the third-generation neutron spallation target for the CERN’s n_TOF facility

The neutron Time-Of-Flight (n_TOF) facility at the European Laboratory for Particle Physics (CERN) is a pulsed white-spectrum neutron spallation source producing neutrons for two experimental areas: EAR1, located 185 m downstream of the spallation target, and EAR2, located 20 m above the target. The facility is based on a lead target impacted by a high-intensity 20 GeV/c proton beam. It is designed to study neutron-nucleus interactions for neutron kinetic energies from a few meV to several GeV, with applications in nuclear astrophysics, nuclear technology, and medical research. The facility is undergoing a major upgrade in 2019–2020, which will include the installation of the new third-generation target. The second-generation target consists in a water-cooled lead cylinder, while the new target will be cooled by nitrogen to avoid erosion-corrosion phenomena and contamination of the cooling water with radioactive lead spallation products. The new design will be optimized also for the vertical flight path. The operation of the new spallation target will start in 2021. This paper presents an overview on the evolution of the design and on the related R&D activities (including beam irradiation tests) carried out to ensure the best performance for both experimental areas and avoid the contamination issues of the previous targets.

Wiederverwertung ausgehobener Molasse basierend auf geologischer Untergrundmodellierung für den geplanten 100 km Teilchenbeschleuniger-Tunnel am CERN nahe Genf, Schweiz

ZusammenfassungDas CERN (Conseil Européen pour la Recherche Nucléaire bzw. European Laboratory for Particle Physics) ist eine weltweit führende internationale Forschungseinrichtung auf dem Gebiet der Hochenergie- und Teilchenphysik. Die Erforschung der grundlegenden Bausteine des Universums und ihrer Interaktionen lieferte in den vergangenen Jahrzehnten bahnbrechende Erkenntnisse, die im experimentellen Nachweis des Higgs-Boson im Juli 2012 gipfelten. Um die in diesem Zusammenhang erforschten Erkenntnisse weiter zu vertiefen und noch unbeantwortete Fragen nach dem Ursprung und der Funktion des Universums zu beantworten, hat eine internationale Gemeinschaft von über 150 Instituten weltweit am CERN eine Studie für ein Forschungsprogramm mit einer neuen, leistungsfähigeren Teilchenbeschleunigerinfrastruktur initiiert. Die Future Circular Collider (FCC) Studie schließt die dafür erforderlichen unterirdischen Tunnel, Kavernen und Schächte und die damit verbundenen Konstruktionen an der Oberfläche mit ein. Die Infrastruktur ist so ausgelegt, um im Zusammenschluss mit den bereits bestehenden Teilchenbeschleunigern am CERN (z. B. PSB, PS, SPS, LHC) zu funktionieren. Im Rahmen des Projekts wurden seit 2014 die ersten technischen Machbarkeitsstudien in den verschiedensten Gebieten, unter anderem Geologie und Konstruktion des Tunnels, der sich über ca. 100 km im teils westschweizerischen und teils französischen Molassebecken erstreckt, durchgeführt, sodass FCC nach derzeitigem Planungsstand um das Jahr 2040 in Betrieb gehen kann. Im Zuge dessen ist ein geologisches Untergrundmodell unerlässlich, um einen sicheren Bau unterirdischer Infrastruktur zu gewährleisten und die Baumethode auf die Geologie abzustimmen. Ein entscheidender Faktor neben dem geologischen Modell ist die Wiederverwertbarkeit des ausgehobenen Molasse-Materials mit einem Volumen von etwa 9 Mio. m3 sowohl aus technischer als auch rechtlicher, gesellschaftspolitischer und sozio-ökonomischer Sicht.Dieser Artikel soll einen Einblick in diese beiden Machbarkeitsstudien des FCC Projekts geben, sowie Ansätze der geologischen, petrophysikalischen, geotechnischen und mineralogisch-chemischen Analysen präsentieren, die zur Beantwortung der Wiederverwertung dienen und in weiterer Folge in das geologische Untergrundmodell einfließen werden.

Federation of European Laboratory Animal Science Associations recommendations of best practices for the health management of ruminants and pigs used for scientific and educational purposes

Most ruminants and pigs used for scientific and educational aims are bred not for these purposes but in a farm environment. Given the wide range of diseases that these species might have, ensuring that the animals’ health status is appropriate can be complex and challenging. The Federation of European Laboratory Animal Science Associations has previously published recommendations for the health monitoring of experimental colonies of pigs (1998) and, respectively, calves, sheep and goats (2000). Unfortunately, the uptake of those recommendations was poor and insufficiently reported in scientific publications. These new recommendations for best practice focus on the main species of ruminants (cattle, sheep and goats) and pigs. They provide general and specific information helpful for designing a health management programme for the suppliers and for the user establishments, as well as guidance on animal procurement. Critical thinking based on the fields of use of the animals is promoted, aiming to help in taking informed decisions rather than establishing an exhaustive exclusion list for pathogens. Implementing the best health and welfare management practices should be done under the guidance of a competent attending veterinarian, with expertise and sufficient authority to take the appropriate action, doubled by excellent communication skills. It is strongly recommended that the user establishment’s veterinarian works in close collaboration with the supplier’s veterinarian.