Democratizing knowledge representation with BioCypher

Sebastian Lobentanzer¹, Patrick Aloy^{2

3}, Jan Baumbach⁴, Balazs Bohar^{5

6}, Vincent J Carey⁷, Pornpimol Charoentong^{8

9}, Katharina Danhauser¹⁰, Tunca Doğan^{11

12}, Johann Dreo^{13

14}, Ian Dunham^{15

16}, Elias Farr¹⁷, Adrià Fernandez-Torras², Benjamin M Gyori¹⁸, Michael Hartung⁴, Charles Tapley Hoyt¹⁸, Christoph Klein¹⁰, Tamas Korcsmaros^{5

19

20}, Andreas Maier⁴, Matthias Mann^{21

22}, David Ochoa^{15

16}, Elena Pareja-Lorente², Ferdinand Popp²³, Martin Preusse²⁴, Niklas Probul⁴, Benno Schwikowski¹³, Bünyamin Sen^{11

12}, Maximilian T Strauss²¹, Denes Turei¹⁷, Erva Ulusoy^{11

12}, Dagmar Waltemath²⁵, Judith A H Wodke²⁵, Julio Saez-Rodriguez²⁶

Affiliations

¹ Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany. sebastian.lobentanzer@uni-heidelberg.de.
² Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain.
³ Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
⁴ Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.
⁵ Earlham Institute, Norwich, UK.
⁶ Biological Research Centre, Szeged, Hungary.
⁷ Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Boston, MA, USA.
⁸ Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany.
⁹ Department of Medical Oncology, National Centre for Tumour Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.
¹⁰ Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.
¹¹ Biological Data Science Lab, Department of Computer Engineering, Hacettepe University, Ankara, Turkey.
¹² Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey.
¹³ Computational Systems Biomedicine Lab, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France.
¹⁴ Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France.
¹⁵ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
¹⁶ Open Targets, Wellcome Genome Campus, Hinxton, UK.
¹⁷ Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
¹⁸ Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
¹⁹ Imperial College London, London, UK.
²⁰ Quadram Institute Bioscience, Norwich, UK.
²¹ Proteomics Program, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark.
²² Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
²³ Applied Tumour Immunity Clinical Cooperation Unit, National Centre for Tumour Diseases (NCT), German Cancer Research Centre (DKFZ), Heidelberg, Germany.
²⁴ German Centre for Diabetes Research (DZD), Neuherberg, Germany.
²⁵ Medical Informatics Laboratory, University Medicine Greifswald, Greifswald, Germany.
²⁶ Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany. pub.saez@uni-heidelberg.de.

PMID: 37337100
DOI: 10.1038/s41587-023-01848-y

Democratizing knowledge representation with BioCypher

Sebastian Lobentanzer et al. Nat Biotechnol. 2023 Aug.

. 2023 Aug;41(8):1056-1059.

doi: 10.1038/s41587-023-01848-y.

Authors

Affiliations

¹ Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany. sebastian.lobentanzer@uni-heidelberg.de.
² Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain.
³ Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
⁴ Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.
⁵ Earlham Institute, Norwich, UK.
⁶ Biological Research Centre, Szeged, Hungary.
⁷ Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Boston, MA, USA.
⁸ Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany.
⁹ Department of Medical Oncology, National Centre for Tumour Diseases (NCT), Heidelberg University Hospital (UKHD), Heidelberg, Germany.
¹⁰ Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.
¹¹ Biological Data Science Lab, Department of Computer Engineering, Hacettepe University, Ankara, Turkey.
¹² Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey.
¹³ Computational Systems Biomedicine Lab, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France.
¹⁴ Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France.
¹⁵ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
¹⁶ Open Targets, Wellcome Genome Campus, Hinxton, UK.
¹⁷ Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
¹⁸ Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
¹⁹ Imperial College London, London, UK.
²⁰ Quadram Institute Bioscience, Norwich, UK.
²¹ Proteomics Program, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark.
²² Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
²³ Applied Tumour Immunity Clinical Cooperation Unit, National Centre for Tumour Diseases (NCT), German Cancer Research Centre (DKFZ), Heidelberg, Germany.
²⁴ German Centre for Diabetes Research (DZD), Neuherberg, Germany.
²⁵ Medical Informatics Laboratory, University Medicine Greifswald, Greifswald, Germany.
²⁶ Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany. pub.saez@uni-heidelberg.de.

PMID: 37337100
DOI: 10.1038/s41587-023-01848-y

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References

1. Li, M. M., Huang, K. & Zitnik, M. Nat. Biomed. Eng. 6, 1353–1369 (2022). - DOI - PubMed
1. Fernández-Torras, A., Duran-Frigola, M., Bertoni, M., Locatelli, M. & Aloy, P. Nat. Commun. 13, 5304 (2022). - DOI - PubMed - PMC
1. Tiddi, I. & Schlobach, S. Artif. Intell. 302, 103627 (2022). - DOI
1. Bonner, S. et al. Brief. Bioinform. 23, bbac404 (2022). - DOI - PubMed
1. Callahan, T. J., Tripodi, I. J., Pielke-Lombardo, H. & Hunter, L. E. Annu. Rev. Biomed. Data Sci. 3, 23–41 (2020). - DOI - PubMed - PMC

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Democratizing knowledge representation with BioCypher

Affiliations

Democratizing knowledge representation with BioCypher

Authors

Affiliations

References

Publication types

Grants and funding

LinkOut - more resources

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