Swobup - the Swate OBO Updater to foster the standardization process

Joint efforts of TaskArea 1 (standardization), TaskArea 2 (technical infrastructure) and TaskArea 3 (data stewards, community support) focusing on the optimization of digital workflows in plant sciences, have enabled one of our developers from Freiburg to implement a tool that facilitates the use of the Swate tool. The tool operates in the background on the Swate Database hosted at the DataPLANT site in Tübingen.

Swate is a Swate Workflow Annotation Tool for the Excel spreadsheet application. It aims to provide a low-friction workflow annotation experience that makes the usage of controlled vocabularies (ontologies) as easy and intuitive as possible. It is designed to integrate in the familiar spreadsheet environment that is the center of a great deal of data-focused wetlab work.

Swobup (Swate OBO Updater) is used to synchronize terms in a previously defined OBO file uploaded to a Github repository by an authorized user. Swobup parses the OBO file and incorporates the changes into the Swate database. The user then has the updated terms available in the Swate tool without having to manually enter individual terms.

More in depth information on the tool and its features, the necessary steps for setup and configuration are available on the nfdi4plants GitHub page, which allows posting issues, improvement suggestions or pull requests. Feedback is welcome!


Exchange of ideas on concepts for sustainable operation and community extension

The project coordinator and speaker of DataPLANT had an online meeting with the NFDI representative of the DFG regarding further community involvment and sustainable development of the consortium and the NFDI. In the half hours talk possible ideas got exchanged, how future project applications could foster the developments to support the steadily expanse of the number of researchers represented by the NFDI. This includes the ongoing process of forming consortia as well as the activities within the already funded consortia to increase their outreach. A crucial task of the consortia is to extend their visibility to the entirety of their researchers. This highlights the credibility to represent their respective fields and establish common standards and concepts. One of the success criteria for the funded consortia is to cover their own specialist community as fully as possible and to network with adjacent research areas. For this purpose, a coordinated onboarding process should be agreed on how new members are formally added to a consortium and incorporated into the governance structure.

Furthermore, a long-term perspective of financial sustainability should be discussed. This could be achieved in part through the design of future funding applications. One way to do this could be through greater involvement of the entire scientific community through the application process and the joint design of data management plans. Consultation with the NFDI could ensure that new projects work according to current workflows, with modern tools and jointly established community standards, and that this is supported in the project process by the NFDI. Such support should function independently of the specific federation process of the individual NFDI consortia and the initial group of co-applicants and participants.

Strategic considerations for future development include recommendations that should be made to future research and collaborative projects. Such projects typically require advice and support in the various aspects of data management, handling tools and workflows, and technical infrastructure. In order to be able to respond flexibly in this regard, a significant amount of staff should be earmarked for community support through, for example, data stewards. This support will be distributed among the original co-applicants according to a key defined in the consortium. However, in addition, research groups starting at a later point in time should also benefit from the NFDI support. Therefore, it needs to be discussed what conditions should be attached to inclusion and in particular how new groups could contribute additional resources needed accordingly. This discussion will be brought forward together with the other NFDI consortia as well through regular exchange e.g. via the speakers meetings with the NFDI directorate.


Virtual exchange between NFDI4BioDiversity and DataPLANT

Envisioning the collaboration within all NFDI-consortia, members of NFDI4BioDiversity and DataPLANT met at the behinning of the new year for a virtual exchange to discuss cross-cutting issues such as standardization, teaching and qualification, common base level infrastructure, the role of data experts and support in research data management, sustainable financing and consortia extension strategies and common strategies of life sciences-related NFDI consortia. 

The conversation on the challenging topic of standardization made the common vision clear that the goal is rather to help users to find existing standards than developing new ones. The objective of DataPLANT is to allow researchers in the lab a convenient ontology extension without having to contact standardization committees. Both consortia will cooperate on standards development in the field of plant biology and tools in the future.

Furthermore, NFDI4BioDiversity convinces with its expertise in the field of data training of junior scientists, even if it is no concrete formation yet. However, we are sure that with combined efforts a great concept for a professional training of so-called "DataStewards" can be created and implemented.

Both consortia, like others in the field of life sciences, depend for their infrastructure on the de.NBI cloud, which provides compute and storage hardware in various forms on which to execute workflows and manage (large scale) data sets. The long term perspective of this resource in respect to the NFDI still needs to be refined.

When considering a sustainable NFDI, it came up that a central HR pool would be advantageous for a proper support of new participants. The community could make use of it if supported by the DFG through future grant applications. For the moment, this idea remains a conceptional construct that needs to be substantiated after consultation with the  appropriate contributors.

In any case, the meeting has encouraged to tackle difficult topics jointly and helped to identify the respective counterparts within both consortia. We look forward to a follow-up exchange.