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Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data2022 Journal of Biomedical Semantics article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Rajaram Kaliyaperumal, Mark D. Wilkinson, Pablo Alarcón Moreno, Nirupama Benis, Ronald Cornet, Bruna dos Santos Vieira, +13 more
48citations -
FAIR GraphRAG: A Retrieval-Augmented Generation Approach for Semantic Data Analysis2025 IEEE International Conference on Knowledge Graph (ICKG) conference-paper Computer Science Research Data Management Practices Open access
Marlena Flüh, Soo-Yon Kim, Carolin Victoria Schneider, Sandra Geisler
1citations -
Semantic modelling of Common Data Elements for Rare Disease registries, and a prototype workflow for their deployment over registry data2021 medRxiv preprint Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Rajaram Kaliyaperumal, Mark D. Wilkinson, Pablo Alarcón Moreno, Nirupama Benis, Ronald Cornet, Bruna dos Santos Vieira, +12 more
9citations -
De-novo FAIRification via an Electronic Data Capture system by automated transformation of filled electronic Case Report Forms into machine-readable data2021 Journal of Biomedical Informatics article Computer Science Research Data Management Practices Open access
Martijn G. Kersloot, Annika Jacobsen, Karlijn H.J. Groenen, Bruna dos Santos Vieira, Rajaram Kaliyaperumal, Ameen Abu–Hanna, +5 more
28citations -
Data harmonization and federated learning for multi-cohort dementia research using the OMOP common data model: A Netherlands consortium of dementia cohorts case study2024 Journal of Biomedical Informatics article Computer Science Privacy-Preserving Technologies in Data Open access
Pedro Mateus, Justine E. F. Moonen, Magdalena Beran, Eva A. Jaarsma, Sophie M. van der Landen, Joost Heuvelink, +11 more
31citations -
De-identifying Clinical Texts using Biomed-Clinical BERTs and Comprehensive Risk Assessment2025 IEEE International Conference on Healthcare Informatics (ICHI) conference-paper Computer Science Privacy-Preserving Technologies in Data Open access
Dhivin Shaji, Lifeng Han, Warren Del-Pinto, Goran Nenadić, Suzan Verberne
1citations -
MedMNIST v2 - A large-scale lightweight benchmark for 2D and 3D biomedical image classification2023 Scientific Data data-paper Computer Science Advanced Neural Network Applications Open access cited by 1 patent
Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Hanspeter Pfister, +1 more
1,037citations -
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic2022 Journal of Biomedical Semantics article Computer Science Research Data Management Practices Open access
Núria Queralt-Rosiñach, Rajaram Kaliyaperumal, César H. Bernabé, Qinqin Long, Simone A. Joosten, Erik L.A. Flikkenschild, +3 more
67citations -
The use of foundational ontologies in biomedical research2023 Journal of Biomedical Semantics article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
César H. Bernabé, Núria Queralt-Rosiñach, Vítor E. Silva Souza, Luiz Olavo Bonino da Silva Santos, Barend Mons, Annika Jacobsen, +1 more
24citations -
Biomedical Entity Linking for Dutch: Fine-tuning a Self-alignment BERT Model on an Automatically Generated Wikipedia Corpus2024 Language Resources and Evaluation Conference (LREC) conference-paper Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Fons Hartendorp, Tom M Seinen, Erik M. van Mulligen, Suzan Verberne
1citations -
MedMNIST: 18x Standardized Datasets for 2D and 3D Biomedical Image Classification2024 Zenodo (CERN European Organization for Nuclear Research) dataset Computer Science Advanced Neural Network Applications Open access
Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Fan Zhao, Hanspeter Pfister, +1 more
0citations -
MedMNIST v2: A Large-Scale Lightweight Benchmark for 2D and 3D Biomedical Image Classification2022 Zenodo (CERN European Organization for Nuclear Research) dataset Computer Science Advanced Neural Network Applications Open access
Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Hanspeter Pfister, +1 more
0citations -
MedMNIST v2: A Large-Scale Lightweight Benchmark for 2D and 3D Biomedical Image Classification2021 Zenodo (CERN European Organization for Nuclear Research) dataset Computer Science Advanced Neural Network Applications Open access
Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Hanspeter Pfister, +1 more
2citations -
The GA4GH Phenopacket schema defines a computable representation of clinical data2022 Nature Biotechnology article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access cited by 2 patents
Julius O.B. Jacobsen, Michael Baudis, Gareth S Baynam, J. Beckmann, Sergi Beltrán, Orion J. Buske, +60 more
117citations -
Improving the Quality of Unstructured Cancer Data Using Large Language Models: A German Oncological Case Study2024 Studies in health technology and informatics book-chapter Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Yongli Mou, J. Lehmkuhl, Nicolas Sauerbrunn, Anja Köchel, Jens Panse, Daniel Truh, +3 more
3citations -
CDE-Mapper: Using retrieval-augmented language models for linking clinical data elements to controlled vocabularies2025 Computers in Biology and Medicine article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Komal Gilani, Marlo Verket, Michel J. Dumontier, Hans‐Peter Brunner‐La Rocca, Visara Urovi
4citations