NFDI4Immuno - All-Hands Meeting 2025

Contribution List

1. TA1/2

Ulrik Stervbo (Ruhr-Universität Bochum)

22/04/2025, 14:20

Report

Reporting

2. TA3

Ralf Kueppers (Universität Duisburg-Essen)

22/04/2025, 14:45

Report

Reporting

3. TA4

Christian Busse (German Cancer Research Center (DKFZ))

22/04/2025, 15:10

Report

Reporting

4. TA5

Mariama Jaiteh (Helmholtz-Centre for Infection Research (HZI))

22/04/2025, 15:35

Report

Reporting

5. State of the NFDI

Christian Busse (German Cancer Research Center (DKFZ))

22/04/2025, 16:30

Report

Reporting

6. Reporting and extension application

Christian Busse (German Cancer Research Center (DKFZ))

22/04/2025, 17:00

Report

Reporting

20. API needs and development

23/04/2025, 09:15

Workshop

Workshop

As we will move closer towards a MVP, we will need an API for submission and later for search and retrieval - first for non-human data. The breakout session could discuss:

• Which stages would the API development move through
• What is required of the model/schema for each stage
• What is required for end-2-end testing of the API at the different stages
• When does it make sense to start...

25. Connecting data analysis tools to the Data portal

23/04/2025, 09:15

Breakout session

Breakout

During this session, we would like to present our current tools and discuss their integration into the future website and portal. We will present a use case of Hyphasma and showcase how nf-core/airrflow operates. nf-core/airrflow is a bioinformatics pipeline dedicated to the analysis or B or T-cell repertoire sequencing data. Hyphasma is a computational tool which allows the simulation of...

23. How is our hardware architecture structured?

23/04/2025, 09:15

Breakout session

Breakout

On which servers are the different data types stored, and who is responsible for this? On which server should the search portal operate?

21. Integration of validated JSON files, the database and web portal

23/04/2025, 09:30

Workshop

Workshop

Which software is intended for the database and the web portal and whether specific requirements for the JSON formats can be derived from it. Do we need to define specifications for JSON, the web portal, and the database in advance to ensure smooth integration later?

31. How to coordinate TAs' work around the data flow

23/04/2025, 11:15

Breakout session

Breakout

(This has been split-off from contribution #24)
As the interfaces cannot be completely specified in the short time available, contact is established between a responsible person from the respective TA so that these two people can coordinate the jointly used interface at short notice at any time.

24. Thinking from the end: Design and interoperability of a user interface

23/04/2025, 11:15

Workshop

Workshop

In this session we want to create/discuss mockups for a user interface and run through certain use cases from the user's perspective.
Interfaces between the TAs and the user interface will also be specified.
In other words: Which data exactly should be transferred between the TAs, in which format, using which technology, and who is responsible for delivering which part, and how exactly.

27. TS4NFDI: Harmonizing Terminology Services within NFDI

23/04/2025, 11:15

Breakout session

Breakout

Goal of TS4NFDI

An overarching research data management across all domains is built upon metadata describing research data and their generation. To make sure that disciplines can create and share a common understanding of the concepts and relations used to describe data, we need terminologies as a formal representation of domain knowledge. Terminology Services 4 NFDI (TS4NFDI) provides...

22. Intensification of collaboration between the individual TAs?

23/04/2025, 11:30

Breakout session

Breakout

Are there any needs for stronger collaboration between the individual TAs?
For example, does TA3 require information from TA1/TA2 to develop training sessions or update our website? Or should TA1/TA2 work more closely with TA4 to ensure that the transpiled and validated metadata is better integrated into the database?

17. Life Science Ontologies

23/04/2025, 12:00

Breakout session

Breakout

The number of available ontologies is daunting, and some are clearly more complete than others and some are better than others (what ever 'better' means).

A break out session on ontologies could address one or more of the questions:

• What is the overlap in needed ontologies between our close-friends consortia?
• How does interoperability between ontologies work?
• How can 'good' and...

18. Metadata interoperability within NFDI

23/04/2025, 14:00

Breakout session

Breakout

Synthesis (see below for original proposals): Interoperability of metadata across consortia is one of the key tasks of NFDI. Therefore the work of TA1/TA2 needs to be in line with various other NFDI activites:

• BioMed Interoperability group
• Section Metadata, its working groups and Task Force Metadata
• Base services relating to metadata (e.g. TS4NFDI)

In this session we will...

19. Test dataset

23/04/2025, 14:00

Breakout session

Breakout

We may benefit from having minimal yet complete datasets for different use cases. The aim of the breakout session would be to open a discussion on a centralized set of test data, that are not based on the developed schemas, but stem from actual laboratory work and will be used to capture any obvious shortcomings as we develop NFDI4Immuno.

The breakout session could address the...

26. Defining a limited set of impactful data analysis tools to implement

23/04/2025, 16:05

Plenary

Plenary

Resulting from our internal survey about the user needs, we were unable to derive a clear answer on which tools shall be implemented to tackle the main pain points of the community. With this virtual session, we would like to run a follow up survey in which we intend to identify a set of 4-5 most valuable and impactful tools according to our consortium.

29. NFDI4Biodiversity

Barbara Ebert (GFBio e.V.)

23/04/2025, 16:15

Plenary

Plenary

7. Breakout - Tools & Workflows

Mariama Jaiteh (Helmholtz-Centre for Infection Research (HZI))

24/04/2025, 09:15

Report

Breakout

12. Breakout - Infrastructure layer

Christian Busse (German Cancer Research Center (DKFZ))

24/04/2025, 09:25

Report

Breakout

10. Breakout - Terminologies & Ontologies

Ulrik Stervbo (Ruhr-Universität Bochum)

24/04/2025, 09:35

Report

Breakout

9. Breakout - Internal organization

Sebastian Ferrara (Deutsches Rheuma-Forschungszentrum Berlin (DRFZ))

24/04/2025, 09:45

Report

Breakout

11. Breakout - Metadata interoperability

Katherina Siewert (German Federal Institute for Risk Assessment)

24/04/2025, 09:55

Breakout

8. Breakout - Data

Anca Dorhoi

24/04/2025, 10:05

Report

Breakout

30. Plenary - Tool survey

Charlyn Dornte (Universitätsklinikum Essen - Institut für Zellbiologie (Tumorforschung)), Mariama Jaiteh (Helmholtz-Centre for Infection Research (HZI))

24/04/2025, 10:15

Report

Breakout

28. Workshop - Workflow integration

Christian Busse (German Cancer Research Center (DKFZ))

24/04/2025, 10:25

Report

Breakout