Overview of available tools and services for early data mobilization

In recent years, the availability of biodiversity data has improved considerably, which has led to an increasing demand for methods and tools for Early Data Mobilization. This term refers to the rapid and efficient processing and analysis of data to gain valuable knowledge and insights before the data is fully available. Also, open educational resources (OER) are available to further early career scientists’ ability to work with data or enable PIs and Postdocs to teach good data management practices. NFDI4Biodiversity, a consortium in the German National Research Data Infrastructure, aims to further improve the availability of such tools for early data mobilization and analysis to facilitate the creation of FAIR Data in biodiversity research and related fields.

The focus of the tools and services collected in this article lies on Early Data Mobilization. These tools should ultimately prepare the data which are collected, created, and/or processed to seamlessly be integrated into the NFDI4Biodiversity’s Research Data Commons (RDC) infrastructure. 

The RDC is conceptualised as an expandable, cloud-based research infrastructure that provides scientists, data providers, and data consumers with powerful tools for creating FAIR data products and facilitates the exchange of data and services in a collaborative manner, both within the German National Research Data Infrastructure (NFDI) and beyond. It is currently in a midstage development state and available for pilot implementations of software tools and data resources. 

Therefore, NFDI4Biodiversity supports data producers, i.e. researchers and consortia participant facilities that provides data or metadata to be distributed to data users by

1. Creating awareness for existing tools which are better suited towards the above goals compared to spreadsheet software as well as tools that enhance spreadsheet software by, e.g. including easier metadata annotation etc.
2. Providing custom training and facilitating IT-support in tool development, deployment and use via the NFDI4Biodiversity Helpdesk 
3. Enabling direct, problem-specific tool development

The following community demands/needs regarding data mobilization will be addressed:

1. Gathering, structuring and managing raw data
2. Workflow realization
3. Quality control and plausibility assurance
4. Analysis and modelling of data
5. Virtual research environments for networking and sharing
6. Data publication
7. Long-term archiving

This article serves to provide an overview of current tools which fulfil the above criteria and are as generic as possible yet as specific as necessary, to help a wide variety of users from different disciplines and remain maintainable and interoperable. In addition to the tools, the article provides an overview of appropriate eductational resources. All tools and resources are mapped to the NFDI4Biodiversity personas who represent the target groups for the service.

During its initial five-year funding period, NFDI4Biodiversity successfully engaged 50 partner institutions, including scientific organizations, museums, natural history societies, and government offices. This collaboration aimed to facilitate the creation and adaptation of research tools for implementation in their respective projects. The following is an overview of tools considered to be especially useful in the early phase of data mobilization within a project’s life cycle. For services supported by NFDI4Biodiversity, i.e. those provided by the consortium partners, the NFDI4Biodiversity Helpdesk is always a first point of contact.

NFDI4Biodiversity  already provides a wide variety of useful tools for early project data mobilization, many of which go beyond the initial stages of the data life cycle. Data provision can be handled by BEXIS2 and RightField opens the door for researchers, who have not yet dismissed the spreadsheet but want to implement the FAIR principles into their work. The Biodiversity Workbench and BioMe on the other hand provide powerful frameworks to manage data, from their collection until the end of the project, providing necessary functionality at the early stages that will be relevant when data will be published or shared eventually. However, these tools are not yet incorporated into the aforementioned Research Data Commons infrastructure.

 Services for Early Data Mobilization from related NFDI consortia

The overall goal of the NFDI is to increase awareness for the importance of research data and research data management and to establish infrastructure, services and tools to ultimately create workflows and automated processes for researchers within and beyond different scientific disciplines. Nomad and the PLANTDataHub work adjacent to the idea of NFDI4Biodiversity’s Research Data Commons, by providing infrastructure that combines several aspects from different phases of the data life cycle. NOMAD and the PLANTDataHub are already usable for scientists from the respective disciplines. Experiences from the development, initialisation and subsequent community acceptance of these services can be useful in establishing and further developing the Research Data Commons platform within the discipline of biodiversity science. ELNs are a tool to overhaul the way data is traditionally collected and processed. This entails the development of suitable software, the allocation of storage space on (locally) hosted servers for the collected data that are available long term, secure and maintainable,  but also the availability of input devices which, especially in biodiversity sciences, need to be able to withstand fieldwork and laboratory conditions. Currency ELNs remain individual solutions for local institutions. These are just a few highlights of services other consortia provide, mainly for their own community. Not mentioned here are knowledge bases many consortia provide to explain and guide users regarding research data management. The project base4NFDI tries to consolidate a lot of services from the different consortia into single access points but does not yet focus on tools concerning  early data mobilization.

State Initiatives, forschungsdaten.info, and the DINI/nestor AG Forschungsdaten

Of the 16 states of Germany, only two do not have a dedicated state initiative working on research data management, support and infrastructure. Only 6 of those offer an ELN, often in direct cooperation with a local university where the instance is hosted. Additionally a variety of services, ranging from certification courses, Research Data Management (RDM) consultations, events, Repositories and many more are provided. The visibility of these state initiatives also varies.

forschungsdaten.info is a portal for RDM related knowledge. It bundles information about the state initiatives, the NFDI consortia, international infrastructures, their tools and services, as well as some basic introductory information regarding RDM. The website is maintained by a national team of RDM specialists.

The UAG Schulung und Fortbildung of the DINI/nestor AG Forschungsdaten provides a comprehensive workshop concept (meant to train RDM trainers), which is modular, expandable and can easily be adapted to teach researchers, whose main focus will not be on teaching RDM, but on using RDM within their research.

Educational resources and miscellaneous services

NFDI4Biodiversity

In support of students and early-career scientists who want to learn the basics of RDM we provide an open educational resource on the topic research data management (Selbstlerneinheit), containing valuable information on all stages of the data life cycle. This is the easiest entry point into RDM, as it will provide a basic understanding and be a guide for further reading. Additionally, NFDI4Biodiversity supports teachers and students of RDM with video series published on Youtube, with topics ranging from Basics of RDM, services provided and tutorials on how to use them, as well as the handling of data in general. The consortium provides GitHub Repositories usable as working environments for Jupyter, R and data validation in PANGAEA, and a Zenodo-Community where slides and other material is published for reuse.

NFDI4Biodiversity provides custom trainings for biodiversity related institutions, working groups and projects on the following topics:

• Creating a Data Management Plan (DMP)
• Data annotation
• Data publication
• Data archiving
• Data submission via Data Submission Service
• Metadata standards
• Legal aspects in research data management (see also the Podcast "Rechtsdschungel")
• Naming conventions and taxonomic harmonization
• Legal regulations for handling biodiversity and environmental data
• Introductions to working with our tools and services
• Fundamentals of research data management and data literacy
• General introduction to NFDI4Biodiversity and the National Research Data Infrastructure (NFDI)

We also provide annual Seasonal Schools for PhD students, researchers, data collectors or data center staff members, offering a broad range of basic and advanced knowledge in the management of biodiversity, ecology and environmental data. The intensive courses include input presentations from experts and hands-on exercises and are tailored to the attendees prior expertise. The Seasonal Schools are designed to create an open, collaborative environment that invites networking and knowledge sharing among participants and can therefore facilitate early data mobilization by furthering the participants knowledge on available tools and services, workflows and best practices.

• A template has been published on Zenodo and can help to set up similar Seasonal Schools:
  • Röder, J., Fischer, M., Tschink, D., & Brand, O. (2023). Template for the NFDI4Biodiversity & GfÖ Winter School. Zenodo. https://doi.org/10.5281/zenodo.8272156
• For basic RDM skills, a self-learning course is available as LiaScript, PDF and in an Ilias version at the University of Marburg. It can also be implemented in other learning environments:
  • Fischer, M., Röder, J., Signer, J., Tschink, D., Weibulat, T., & Brand, O. (2023, Dezember 14). NFDI4Biodiversity Self-Study Unit - Research Data Management for Biodiversity Data. Zenodo. https://doi.org/10.5281/zenodo.10377868

  • Research Data Management for Biodiversity Data: https://ilias.uni-marburg.de/ilias.php?baseClass=ilrepositorygui&ref_id=3219917

  • LiaScript: https://liascript.github.io/course/?https://raw.githubusercontent.com/NFDI4Biodiversity/nfdi4biodiversity-sle/main/README.md#1

More educational resources as well as information about events can be found on the NFDI4Biodiversity website and its Knowledge Base. If you want to stay up to date regarding training developements in the life sciences, consider subscribing to the trainings4lifescience mailinglist.

Other relevant NFDI Consortia and adjacent Infrastructures