Was wir tun

The poster has been created for and shown at the first European conference of the BMBF Research Initiative for the Conservation of Biodiversity (FEdA) Biodiversity and Human Well-Being – Europe’s Role in Shaping Our Future from November 9th - 11th, 2022.

The National Research Data Infrastructure (NFDI) and FEdA started at about the same time in 2020. Given the importance attributed to the availability of FEdA research outputs, including data, the speakers of the two initiatives quickly decided to join forces. A FEdA data policy was established for the projects and a support workflow was set up. The FEdA Coordination Office is the initial point of contact, with data experts from NFDI in the background for requests regarding specific data types and community standards.

Linares, Jimena, Ebert, Barbara, Eberhardt, Jan, Frohne, Katharina, Sauerland, Kristin, Mozygemba, Kati, & Miller, Bernhard. (2023). Collaborative Research Data Management Support for FEdA projects. Zenodo: https://doi.org/10.5281/zenodo.7624583

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Changes in organismal abundance and diversity are barely documented. Censuses of species are usually fragmentary and inferred by often spatially, temporally and ecologically unsatisfactory simple species lists for individual study sites. Thus, detrimental global processes and their drivers often remain unrevealed. A major impediment to monitoring species diversity is the lack of human taxonomic expertise that is implicitly required for large-scale and fine-grained assessments. Another is the large amount of personnel and associated costs needed to cover large scales, or the inaccessibility of remote but nonetheless affected areas. To overcome these limitations we propose a network of Automated Multisensor stations for Monitoring of species Diversity (AMMODs) to pave the way for a new generation of biodiversity assessment centers. This network combines cutting-edge technologies with biodiversity informatics and expert systems that conserve expert knowledge. Each AMMOD station combines autonomous samplers for insects, pollen and spores, audio recorders for vocalizing animals, sensors for volatile organic compounds emitted by plants (pVOCs) and camera traps for mammals and small invertebrates. AMMODs are largely self-containing and have the ability to pre-process data (e.g. for noise filtering) prior to transmission to receiver stations for storage, integration and analyses. Installation on sites that are difficult to access require a sophisticated and challenging system design with optimum balance between power requirements, bandwidth for data transmission, required service, and operation under all environmental conditions for years. An important prerequisite for automated species identification are databases of DNA barcodes, animal sounds, for pVOCs, and images used as training data for automated species identification. AMMOD stations thus become a key component to advance the field of biodiversity monitoring for research and policy by delivering biodiversity data at an unprecedented spatial and temporal resolution.

J. Wolfgang Wägele, Paul Bodesheim, Sarah J. Bourlat, Joachim Denzler, Michael Diepenbroek, Vera Fonseca, Karl-Heinz Frommolt, Matthias F. Geiger, Birgit Gemeinholzer, Frank Oliver Glöckner, Timm Haucke, Ameli Kirse, Alexander Kölpin, Ivaylo Kostadinov, Hjalmar S. Kühl, Frank Kurth, Mario Lasseck, Sascha Liedke, Florian Losch, Sandra Müller, Natalia Petrovskaya, Krzysztof Piotrowski, Bernd Radig, Christoph Scherber, Lukas Schoppmann, Jan Schulz, Volker Steinhage, Georg F. Tschan, Wolfgang Vautz, Domenico Velotto, Maximilian Weigend, Stefan Wildermann (2022): Towards a multisensor station for automated biodiversity monitoring, Basic and Applied Ecology, https://doi.org/10.1016/j.baae.2022.01.003 .

Die Stellungnahme mit Positionen zur Etablierung von NFDI-weiten Basisdiensten richtet die Konsortialversammlung des NFDI e.V. an die Entscheidungsträger:innen in den NFDI-Gremien, bei der Deutschen Forschungsgemeinschaft (DFG) und in der Gemeinsamen Wissenschaftskonferenz (GWK).
Die Konsortialversammlung benennt Faktoren für eine gelingende Implementierung von Basisdiensten und schlägt den Entscheidungsträger:innen drei – auch miteinander kombinierbare Optionen für die Realisierung von NFDI-weiten Basisdiensten vor: (1) Flexible begleitende  Förderformate für Basisdienste, (2) Aufbau der Basisdienste über Fachkonsortien, (3) ein gemeinsam aus dem NFDI e.V. heraus getragenes Basisdienst-Konsortium.

Konsortialversammlung des Vereins Nationale Forschungsdateninfrastruktur (NFDI) e.V. (2022). Stellungnahme der NFDI-Konsortien zu Basisdiensten. Zenodo. https://doi.org/10.5281/zenodo.6091657

Im Rahmen der Data-Talk-Reihe der Hessischen Forschungsdateninfrastrukturen (HeFDI) stellt Prof. Dr. Frank Oliver Glöckner (Universität Bremen, Alfred-Wegener-Institut Bremerhaven und GFBio e.V.), Sprecher von NFDI4Biodiversity, die Aufgaben und Services des Konsortiums vor.

Glöckner, Frank Oliver. (2022, February 15). NFDI4Biodiversity – Biodiversity, Ecology and Environmental Data. HeFDI Data Talks, Philipps-Universität Marburg. Zenodo. https://doi.org/10.5281/zenodo.6087255

Das hier vorgelegte Sektionskonzept spezifiziert Arbeitspakete zum Aufbau von gemeinschaftlich genutzten und vernetzten Informationsinfrastrukturen und benennt konkrete Elemente, die für die angestrebte Interoperabilität innerhalb der NFDI und darüber hinaus benötigt werden. Zudem wird vorgeschlagen, mit Blick auf die geplante Strukturevaluation Bedarfe und offene To Dos zur Sicherung und zum langfristigen Betrieb der in die NFDI eingebrachten Ressourcen und Dienste zu beleuchten (Stichwort Nachhaltigkeit).

Die Sektion organisiert die Abstimmung der NFDI-Konsortien und weiterer Akteure zur Entwicklung von Infrastrukturen und Software-Komponenten. Die Sektion ist damit zentraler Ansprechpartner für den Aufbau möglicher Basisdienste.

Ganz konkret wird die Sektion unter anderem an der Realisierung einer multi-cloud-basierten Basis-Infrastruktur arbeiten, die bereits jetzt von mehreren Konsortien unterstützt wird. Die sog. “Research Data Commons” (RDC) soll einen einheitlichen Zugang zu Daten-, Software, und Compute-Ressourcen sowie einen souveränen Datenaustausch und kollaboratives Arbeiten ermöglichen. Mit dem RDC wird ein Paradigmenwechsel von Data zu Function Shipping eingeleitet. NFDI4Biodiversity hat dieses Konzept auch für seine eigene Infrastrukturentwicklung vorgesehen und wirkt aktiv am Aufbau der Sektion mit.

Diepenbroek, Michael, Schimmler, Sonja, & Ebert, Barbara (2021): Sektionskonzept Common Infrastructures zur Einrichtung einer Sektion im Verein Nationale Forschungsdateninfrastruktur (NFDI) e.V. Zenodo, https://doi.org/10.5281/zenodo.5607490

NFDI4BioDiversity ist ein Konsortium innerhalb der Nationalen Forschungsdateninfrastruktur (NFDI) mit einem Schwerpunkt auf Services für die Biodiversitätsforschung und Ökologie. Unzählige Studien belegen den Rückgang der Biodiversität auf unserem Planeten. Drängende Fragen in diesem Zusammenhang sind unter anderem welche Auswirkungen der Rückgang der Biodiversität auf die betroffenen Ökosysteme hat und welche (anthropogenen) Einflüsse die Biodiversität reduzieren oder fördern. Um die komplexen Zusammenhänge zu verstehen und daraus Handlungsempfehlungen abzuleiten, werden vielfältige, qualitätsgesicherte und FAIRe[1] Daten benötigt. Diese umfassen das Vorkommen von Pflanzen, Tieren und Mikroorganismen, einschließlich ihrer genotypischen, phänotypischen und funktionalen Vielfalt, sowie deren Zusammenspiel in Populationen und Ökosystemen. In NFDI4BioDiversity haben sich 49 Partner aus Wissenschaft, Behörden und Bürgerwissenschaften zusammengeschlossen, um die Mobilisierung und Publikation vorhandener Daten voranzutreiben, effiziente Workflows zu entwickeln und Tools und Services zur Unterstützung von Analysen bereitzustellen.

Weber, Judith; Ebert, Barbara; Diepenbroek, Michael; Kostadinov, Ivaylo und Glöckner, Frank Oliver (2021): NFDI4BioDiversity – NFDI-Konsortium für Biodiversitäts-, Ökologische Und Umweltdaten. Bausteine Forschungsdatenmanagement, Nr. 2 (Juli). German: 98-109. DOI: 10.17192/BFDM.2021.2.8334

Knowledge derived from nucleotide sequence data is increasing in importance in the life sciences, as well as decision making (mainly in biodiversity policy). Metadata standards have been established to facilitate sustainable sequence data management according to the FAIR principles (Findability, Accessibility, Interoperability, Reusability). Here, we review the status of metadata available for raw read Illumina amplicon and whole genome shotgun sequencing data derived from ecological metagenomic material that are accessible at the European Nucleotide Archive (ENA), as well as the compliance of the primary sequence data (fastq files) with data submission requirements. While overall basic metadata, such as geographic coordinates, were retrievable in 98% of the cases for this type of sequence data, interoperability was not always ensured and other (mainly conditionally) mandatory parameters were often not provided at all. Metadata standards, such as the ‘Minimum Information about any(x) Sequence (MIxS)’, were only infrequently used despite a demonstrated positive impact on metadata quality. Furthermore, the sequence data itself did not meet the prescribed requirements in 31 out of 39 studies that were manually inspected. To tackle the most immediate needs to improve FAIR sequence data management, we provide a list of minimal suggestions to researchers, research institutions, funding agencies, reviewers, publishers, and databases, that we believe might have a potentially large positive impact on sequence data and metadata FAIRness, which is crucial for further research and its derived applications.

Hassenrück, Christiane; Poprick, Tobias; Helfer, Véronique; Molari, Massimiliano; Meyer, Raissa; Kostadinov, Ivaylo (2021): FAIR enough? A perspective on the status of nucleotide sequence data and metadata on public archives. 24 p; BioRxiv 2021.09.23.461561; doi: https://doi.org/10.1101/2021.09.23.461561

This report outlines the results of a strategy workshop on cross-cutting topics of the National Research Data Infrastructure (NFDI). The workshop took place on 26 August 2020. The participants were the nine consortia from the first of three funding rounds for NFDI and the NFDI Directorate.

The report captures 16 cross-cutting topics upon the workshop participants agreed to be most relevant. In particular, the report shows for each cross-cutting topic: consortia’s intended participation as well as willingness to take a coordination role, expected additional financial requirements, and to which degree further specification is needed.

The results confirm the importance of the cross-cutting topics for NFDI. They can be seen as a preliminary basis for the further addressing of cross-cutting topics in NFDI’s planned inter-consortial sections and working groups, that will also include the consortia of funding rounds two and three.

Ebert, Barbara; Fluck, Juliane; Glöckner, Frank Oliver; Koepler, Oliver, Miller, Bernhard, Schmitt, Robert, Schrade, Torsten, Stegle, Oliver, Steinbeck, Christoph, von Suchodoletz, Dirk, Wagemann, Kurt, Knebes, Jennifer, Kraft, Sophie, Seitz-Moskaliuk, Hendrik, Sure-Vetter, York, & Wössner, Elena. (2021). NFDI Cross-cutting Topics Workshop Report. Zenodo, 14 p.. DOI: 10.5281/zenodo.4593770

Biodiversity is more than just the diversity of living species. It includes genetic and phenotypic diversity of organisms, functional diversity, interactions and the diversity of populations and whole ecosystems. The recent Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) report confirmed that our planet experiences a rapid loss of biodiversity with dramatic consequences for mankind. Answers to scientifically and societal relevant questions can only be found based on the availability of data integrated from multiple sources and building on different knowledge domains in science and society. The FAIR data principles provide a framework towards such integration. To foster access to interoperable data, NFDI4BioDiversity focuses on the following six objectives: 1) Promoting research data management as an integral part of biodiversity research, 2) Enabling FAIRness of data, 3) Consolidating FAIRness with quality, 4) Embedding NFDI4BioDiversity into the (inter-)national landscape, 5) Addressing NFDI-wide cross-cutting topics and 6) Promoting collaborative governance, viability and sustainability of data infrastructure services and science. These objectives are implemented by the NFDI4BioDiversity work programme and its five task areas

Glöckner, Frank Oliver, Diepenbroek, Michael, Felden, Janine, Güntsch, Anton, Stoye, Jens, Overmann, Jörg, Wimmers, Klaus, Kostadinov, Ivaylo, Yahyapour, Ramin, Müller, Wolfgang, Scholz, Uwe, Triebel, Dagmar, Frenzel, Mark, Gemeinholzer, Birgit, Goesmann, Alexander, König-Ries, Birgitta, Bonn, Aletta, & Seeger, Bernhard. (2020). NFDI4BioDiversity – A Consortium for the National Research Data Infrastructure (NFDI). Zenodo, 128 p. DOI: 10.5281/zenodo.3943645