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Published June 19, 2023 | Version v1
Journal article Open

Democratizing knowledge representation with BioCypher

Creators

  • 1. Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
  • 2. Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
  • 3. Institute for Computational Systems Biology, University of Hamburg, Germany
  • 4. Earlham Institute, Norwich, UK; Biological Research Centre, Szeged, Hungary
  • 5. Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Boston, USA
  • 6. Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany; Department of Medical Oncology, National Centre for Tumour Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
  • 7. Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
  • 8. Biological Data Science Lab, Department of Computer Engineering, Hacettepe University, Ankara, Turkey; Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
  • 9. Computational Systems Biomedicine Lab, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France; Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
  • 10. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
  • 11. Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
  • 12. Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
  • 13. Earlham Institute, Norwich, UK; Quadram Institute Bioscience, Norwich, UK
  • 14. Proteomics Program, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
  • 15. Applied Tumour Immunity Clinical Cooperation Unit, National Centre for Tumour Diseases (NCT), German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
  • 16. German Centre for Diabetes Research (DZD), Neuherberg, Germany
  • 17. Computational Systems Biomedicine Lab, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
  • 18. Proteomics Program, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark
  • 19. Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
  • 20. Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany

Description

This is the self-archived version of the article 'Democratizing knowledge representation with BioCypher.' It describes the BioCypher framework, a tool to build grounded knowledge graphs in biomedical science. For more information, see https://biocypher.org.

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democratizing-knowledge-representation-with-biocypher.pdf

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Additional details

Related works

Has version
Preprint: arXiv:2212.13543 (arXiv)
Journal article: https://www.nature.com/articles/s41587-023-01848-y (URL)