NFDI4Microbiota - The German National Research Data Infrastructure for the Research of Microbiota

NFDI4Microbiota - The German National Research Data Infrastructure for the Research of Microbiota Represented by Alice C. McHardy, Alexander Goesmann, Manja Marz, Alexander Sczyrba, Konrad U. Förstner under the National Research Data Infrastructure NFDI 28/1 Project number 460129525 Earth/Climate Agriculture Food Production Biotechnology Pharmaceutics Human well-being Flagship services Critical Assessment of Metagenome Interpretation The Cloud-based Workflow Manager Microbial strain identifier-service Virus metadata, and sequence resource Distributed cloud data orchestration solution NFDI4Microbiota is a strong contributor to Base4NFDI International collaborations Training participants >2300 >300 Training events > 190 9 Productive use cases Community engagements 15 Use case collaborating institutions Vision Researchers can translate data easily into a deep understanding of microbial organisms and their interactions on a molecular level. Mission Be the central hub in Germany for supporting the microbiology community with data access, analysis services, data/metadata standards and training. Community & Services Scaling into the community Challenges Impact For example: - Bioinformatical tools including exact version - Dependencies - Reference data (genomes) For example: - Media composition - pH value - Temperature - Geo location - Sample depth For example: - Machine type - Vendor - Firmware version - Run parameters Storage Collection of technical and biological metadata Knowledge base and training Consultation / Helpdesk Electronic lab notebooks (ELNs) Data quality control Standard operating procedures (SOPs) Data bases and knowledge graphs Data management plans (DMPs) Study design Data generation Data analysis Publication / submission of data / code / models to repositories (ENA/SRA/Zenodo etc.) NFDI4Microbiota Services Experiments High throughput methods Example use case: MetaProt - Functional profiling and routine diagnosis of humane microbiomes by metaproteomics Metaproteomics enables in-depth microbiome analysis, especially in the human gut, using LC-MS / MS to characterize taxonomic and functional composition. Protein abundance reflects activity and can detect host or environmental proteins. Use Case MetaProt focuses on standardization and data integration by: - Developing a curated human gut microbiome protein database - Creating a tool for metadata annotation and standardized file conversion 4000 Compute cores 350 TB storage 500 TB object storage Projects > 200 TB research data > 38 >40 Curated best practice workflows Achievements Highlights of the next funding phase LEAD USE CASE RDMT4 PID4 LEAD INCUBATOR KGI4 IAM4 MEMBER USED IN TRAINING DMP4 Jupyter4 EXCHANGE TS4 LEAD MC4 USER / CONTRIBUTOR software USER / CONTRIBUTOR DALIA4 Customized training programmes for research networks and institutions FAIR Practices Lab Certification Early metadata capturing and integration of data generation facilities (e.g. sequencing centers) This poster is deposited at Zenodo under the DOI: 10.5281/zenodo.17305711 Research workflow Resource requirements for NFDI internal interactions (Sections and Base4NFDI) Seamless integration in heterogeneous research environments Overarching Knowlege Graph Political consulting and legal frameworks regarding digital sequence information (DIS) Expanded support for eukaryotic species (e.g. with the MicrobeDive database) Integration via the Life Science Research Node into the European Open Science Cloud Generating / enhancement of metadata using AI solutions Improving (meta)data for better model training (AI-ready) Deeper collaboration and consolidation with consortia in the BioMed and the Biodata interest groups Creating privacy sensitive data processing and secure processing environments § + Fungi Viruses Archaea Protists Parasites Bacteria Viruses Microbial Communities 13 Researc h Cons o rtia EXC 2051 EXC 2124 EXC 2155 SFB 1182 SFB 1371 SFB 1382 SFB 1583 SFB 2330 SPP 2474 Fraunhofer CIMD Global Microbiome Conservancy Microbes for Climate Research Center One Health Ruhr >60 P ar t ic i pan t s 7 Assoc i ati o ns VAAM GfV DGHM DGP DGfM DMykG EuMik 10 (Co-)Ap p li c an t s Universities Research Institutes Plön Jena Leipzig Berlin P otsdam Essen Aachen Mün c hen Heide l berg K öln Erla n gen Bielefeld W ür z bu r g Ma r bu r g Gießen Kiel B r emen Jülich Brau n sc h weig Hannover K arlsr u he Bonn Hambu r g Da r mstadt F ran k furt Tübingen Stuttgart Regensburg Dortmund Wuppertal Köthen Saarbrücken