MeDaX - bioMedical Data eXploration
ABOUT THE PROJECT
Evidence-based medicine uses high-quality, curated, and reliable data from health research, combines them with the respective individual expertise of the treating physicians and aims to make the best possible treatment decisions for individual patients. In order to generate the necessary knowledge from the accessible data sources, heterogeneous data must be combined and be made comparable – a complex task from the perspective of data sciences. For a reliable data basis of high quality, good documentation of the research process and the resulting data is crucial. This also includes the process of integrating heterogeneous data from different sources, as the quality of the database depends to a large extent on the quality of the data sources, but no less on the quality of the data integration.
MeDaX - bioMedical Data eXploration
GOALS
With a focus on the generation of FAIR data and the integration of standardized data formats, the junior research group MeDaX is developing an information and research platform for (bio)Medical Data eXploration. For this purpose,
- heterogeneous (bio)medical data from various sources are merged into a knowledge graph (graph database) via so-called ETL processes (ETL: Extract-Transform-Load),
- new or improved methods for computer-aided semantic enrichment, quality control, provenance and comparability are developed and
- algorithms and tools for further processing of the data are integrated.
Various data sources, such as the Medical Informatics Initiative core data set, local population studies, biomedical ontologies, and publicly available information portals, will serve as starting points. In addition, the needs of patients and data-collecting physicians and scientists must be elicited during the set-up phase to ensure the greatest possible benefit from the MeDaX platform.
The protection of personal data and the transparent documentation and communication of scientific work as the basis for sustainable science are particularly important to the group.
Achievements and ongoing work
Current work
Upcoming milestones and planned work
Establishing a use case at the DIZ — Retrospective analysis study on graph-based descriptive characterisation of patient cohorts of the University Medical Centres Greifswald and Rostock
Improve Ontology — Restructuring the Biomedical Resource Ontology (BRO)
Applying for grants — Applying for follow-up projects to combine integrated knowledge graphs with mathematical models for improved clinical decision support
Projects in publication process — BRAinS (in revision), MIRAPIE (submitted), FAIR KDS (co-author commenting), MeDaX Pipeline (writing)
MIRAPIE Guideline published
December 2025
MIRAPIE Guideline published on Zenodo, doi: 10.5281/zenodo.17939690
P&B Guideline published
November 2025
P&B Guideline: People-oriented meeting organisation for Beginners published on Zenodo, doi: 10.5281/zenodo.17733934
BRAinS preprint
October 2025
BRAinS: a graph-based analysis and recommendation approach for enhanced health study discoverability, JMIR preprint, doi: 10.2196/preprints.86812
MIRAPIE preprint published
September 2025
MIRAPIE: Proposing a Harmonising Framework as a Minimal Community Standard for Biomedical Provenance Documentation, Preprint with The Lancet, doi: 10.2139/ssrn.5327042
Talk at GMDS 2025
September 2025
Gave a talk about FAIR data management at the AG Datenmanagement at the GMDS 2025 (08.–10.09.2025, Jena, DE)
Workshop at GMDS 2025
September 2025
Workshop on Privacy compliant meeting orga for Beginners at the GMDS 2025 (08.–10.09.2025, Jena, DE)
mdm2neo4j published
May 2025
mdm2neo4j: Generating Graph Representations of Medical Data Models, Studies in Health Technology and Informatics, doi: 10.3233/SHTI250424
Poster at MIE 2025
May 2025
Presented poster on Adopting ontologies: sustainable research reusing the Biomedical Resource Ontology at the MIE 2025 (19th–21st of May, 2025, Glasgow, UK), doi: 10.3233/SHTI250652
MIRAPIE Ontology published
May 2025
MIRAPIE Ontology – MInimal Requirements for Automated Provenance Information Enrichment in biomedical research published on Zenodo, doi: 10.5281/zenodo.15608384
Talk at MIRACUM Kolloquium
May 2025
Presented "Clinical data to knowledge graph: The MeDaX pipeline" at MIRACUM Kolloquium (13/05/2025)
MeDaX pipeline released
April 2025
Software release: MeDaX pipeline, Zenodo, doi: 10.5281/zenodo.15229076
Demo at SWAT4HCLS 2025
February 2025
Gave "Demonstration: The MeDaX-KG on FHIR" at SWAT4HCLS 2025 (24/02/2025, Barcelona)
Testing at the DIZ
November 2024
From this point, we test our pipeline regulary against the census data in our local DIZ.
MeDaX-KG at MIRACUM DIFUTURE Symposium
October 2024
Presented "MeDaX-KG: A knowledge graph on FHIR" at MIRACUM DIFUTURE Symposium (11/10/2024, Munich)
Talk at MIE 2024
June 2024
Presented "MeDaX: A knowledge graph on FHIR" at MIE 2024 (10/06/2024, Athens), doi: 10.3233/SHTI240423
Graph databases systematic review
April 2024
Graph databases in systems biology: a systematic review, Briefings in Bioinformatics, doi: 10.1093/bib/bbae561
FAIR assessment at SWAT4HCLS 2024
February 2024
Presented the FAIR assessment of the MII core data set at the SWAT4HCLS 2024 (26th–29th of Feb, 2024, Leiden, NE), https://ceur-ws.org/Vol-3890/paper-12.pdf
Poster at SWAT4HCLS 2024
February 2024
Presented poster "MeDaX Prototype v0.2" at SWAT4HCLS 2024 (26/02/2024, Leiden)
MeDaX @ MIRACUM-DIFUTURE Symposium
October 2023
Presented the MeDaX project giving a talk at the MIRACUM-DIFUTURE Symposium 2023 (9th–10th of Oct, Erlangen, DE)
FAIRifying community data published
September 2023
Experiences from FAIRifying community data and FAIR infrastructure in biomedical research domains, Proceedings of the Conference on Research Data Infrastructure, doi: 10.52825/cordi.v1i.415
BioCypher paper published
June 2023
Lobentanzer et al. 2023: "Democratizing Knowledge Representation with BioCypher" Nat Biotech 2023;41:1056-1059, doi: 10.1038/s41587-023-01848-y
MeDaX Knowledge Graph Prototype published
May 2023
The MeDaX Knowledge Graph Prototype, Studies in Health Technology and Informatics, doi: 10.3233/SHTI230089
Talk at MIE 2023:
May 2023
Presentation of preliminary work on the FAIR assessment of NUM in a talk, doi: 10.3233/SHTI230251
TAPP published
April 2023
Gierend et al. "TAPP: Defining standard provenance information for clinical research data and workflows - Obstacles and opportunities" WWW '23 Companion: Companion Proceedings of the ACM Web Conference 2023;1551–1554, doi: 10.1145/3543873.3587562
Talk at the COMBINE 2022
October 2022
Presented the MeDaX Vision to the community giving a talk at the COMBINE (Computational Modeling of Biological Networks Meeting, 6th–8th of Oct, 2022, Berlin, DE)
Poster prize
September 2022
The MeDaX Vision poster won a poster prize at the MIRACUM Symposium 2022 (20th–21st of Sept 2022, Gießen, DE)
NEWS
- MILA Seminar - Hristina Uzunova on AI in medical image processing
- MILA-Seminar - Prof. Josephine Thomas on graph neural networks
- Publication - Guideline about privacy-friendly meeting organisation
- MILA-Seminar - SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences
- MILA Seminar - PD Dr. Susanne Neufang on gender bias in AI models