Democratizing knowledge representation with BioCypher

Sebastian Lobentanzer; Patrick Aloy; Jan Baumbach; Balazs Bohar; Vincent J. Carey; Pornpimol Charoentong; Katharina Danhauser; Tunca Doğan; Johann Dreo; Ian Dunham; Elias Farr; Adrià Fernandez-Torras; Benjamin M. Gyori; Michael Hartung; Charles Tapley Hoyt; Christoph Klein; Tamas Korcsmaros; Andreas Maier; Matthias Mann; David Ochoa; Elena Pareja-Lorente; Ferdinand Popp; Martin Preusse; Niklas Probul; Benno Schwikowski; Bünyamin Sen; Maximilian T. Strauss; Denes Turei; Erva Ulusoy; Dagmar Waltemath; Judith A.H. Wodke; Julio Saez-Rodriguez

doi:10.1038/s41587-023-01848-y

Democratizing knowledge representation with BioCypher

Sebastian Lobentanzer
, Patrick Aloy
, Jan Baumbach
, Balazs Bohar
, Vincent J. Carey
, Pornpimol Charoentong
, Katharina Danhauser
, Tunca Doğan
, Johann Dreo
, Ian Dunham
, Elias Farr
, Adrià Fernandez-Torras
, Benjamin M. Gyori
, Michael Hartung
, Charles Tapley Hoyt
, Christoph Klein
, Tamas Korcsmaros
, Andreas Maier
, Matthias Mann
, David Ochoa

Elena Pareja-Lorente, Ferdinand Popp, Martin Preusse, Niklas Probul, Benno Schwikowski, Bünyamin Sen, Maximilian T. Strauss, Denes Turei, Erva Ulusoy, Dagmar Waltemath, Judith A.H. Wodke, Julio Saez-Rodriguez

University Hospital Heidelberg
The Barcelona Institute of Science and Technology
Technology Department
Universität Hamburg
Gut Health and Food Safety Programme
Biological Research Centre
Harvard Medical School
Heidelberg University
Ludwig-Maximilians-Universität München
Hacettepe University
Univ-Paris Diderot Sorbonne Paris-Cité
European Bioinformatics Institute
Open Targets
Harvard Medical School
Imperial College London
Institute of Food Research
University of Copenhagen
Max Planck Institute of Biochemistry
German Cancer Research Center
German Centre for Diabetes Research (DZD)
University Medicine Greifswald

Research output: Contribution to journal › Letter › peer-review

45 Scopus citations

Original language	English
Pages (from-to)	1056-1059
Number of pages	4
Journal	Nature Biotechnology
Volume	41
Issue number	8
DOIs	https://doi.org/10.1038/s41587-023-01848-y
State	Published - Aug 2023
Externally published	Yes

Access to Document

10.1038/s41587-023-01848-y

Cite this

Lobentanzer, S., Aloy, P., Baumbach, J., Bohar, B., Carey, V. J., Charoentong, P., Danhauser, K., Doğan, T., Dreo, J., Dunham, I., Farr, E., Fernandez-Torras, A., Gyori, B. M., Hartung, M., Hoyt, C. T., Klein, C., Korcsmaros, T., Maier, A., Mann, M., ... Saez-Rodriguez, J. (2023). Democratizing knowledge representation with BioCypher. Nature Biotechnology, 41(8), 1056-1059. https://doi.org/10.1038/s41587-023-01848-y

@article{4a57be3dac3f447ab3c9676a4ea8099b,

title = "Democratizing knowledge representation with BioCypher",

author = "Sebastian Lobentanzer and Patrick Aloy and Jan Baumbach and Balazs Bohar and Carey, \{Vincent J.\} and Pornpimol Charoentong and Katharina Danhauser and Tunca Doğan and Johann Dreo and Ian Dunham and Elias Farr and Adri{\`a} Fernandez-Torras and Gyori, \{Benjamin M.\} and Michael Hartung and Hoyt, \{Charles Tapley\} and Christoph Klein and Tamas Korcsmaros and Andreas Maier and Matthias Mann and David Ochoa and Elena Pareja-Lorente and Ferdinand Popp and Martin Preusse and Niklas Probul and Benno Schwikowski and B{\"u}nyamin Sen and Strauss, \{Maximilian T.\} and Denes Turei and Erva Ulusoy and Dagmar Waltemath and Wodke, \{Judith A.H.\} and Julio Saez-Rodriguez",

note = "Funding Information: This project has received funding from the European Union{\textquoteright}s Horizon 2020 research and innovation programme (grant agreement No 965193 (DECIDER) and 116030 (TransQST)), the German Federal Ministry of Education and Research (BMBF, Computational Life Sciences grant No 031L0181B and MSCoreSys research initiative research core SMART-CARE 031L0212A), the US Defense Advanced Research Projects Agency (DARPA) Young Faculty Award (W911NF-20-1-0255), and the Medical Informatics Initiative Germany, MIRACUM consortium (FKZ: 01ZZ2019). We thank Henning Hermjakob, Benjamin Haibe-Kains, Pablo Rodriguez-Mier, Daniel Dimitrov and Olga Ivanova for feedback on the manuscript and Ben Hitz and Pedro Assis for feedback on their use of BioCypher. Funding Information: This project has received funding from the European Union{\textquoteright}s Horizon 2020 research and innovation programme (grant agreement No 965193 (DECIDER) and 116030 (TransQST)), the German Federal Ministry of Education and Research (BMBF, Computational Life Sciences grant No 031L0181B and MSCoreSys research initiative research core SMART-CARE 031L0212A), the US Defense Advanced Research Projects Agency (DARPA) Young Faculty Award (W911NF-20-1-0255), and the Medical Informatics Initiative Germany, MIRACUM consortium (FKZ: 01ZZ2019). We thank Henning Hermjakob, Benjamin Haibe-Kains, Pablo Rodriguez-Mier, Daniel Dimitrov and Olga Ivanova for feedback on the manuscript and Ben Hitz and Pedro Assis for feedback on their use of BioCypher. ",

year = "2023",

month = aug,

doi = "10.1038/s41587-023-01848-y",

language = "English",

volume = "41",

pages = "1056--1059",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Research",

number = "8",

}

Lobentanzer, S, Aloy, P, Baumbach, J, Bohar, B, Carey, VJ, Charoentong, P, Danhauser, K, Doğan, T, Dreo, J, Dunham, I, Farr, E, Fernandez-Torras, A, Gyori, BM, Hartung, M, Hoyt, CT, Klein, C, Korcsmaros, T, Maier, A, Mann, M, Ochoa, D, Pareja-Lorente, E, Popp, F, Preusse, M, Probul, N, Schwikowski, B, Sen, B, Strauss, MT, Turei, D, Ulusoy, E, Waltemath, D, Wodke, JAH & Saez-Rodriguez, J 2023, 'Democratizing knowledge representation with BioCypher', Nature Biotechnology, vol. 41, no. 8, pp. 1056-1059. https://doi.org/10.1038/s41587-023-01848-y

TY - JOUR

T1 - Democratizing knowledge representation with BioCypher

AU - Lobentanzer, Sebastian

AU - Aloy, Patrick

AU - Baumbach, Jan

AU - Bohar, Balazs

AU - Carey, Vincent J.

AU - Charoentong, Pornpimol

AU - Danhauser, Katharina

AU - Doğan, Tunca

AU - Dreo, Johann

AU - Dunham, Ian

AU - Farr, Elias

AU - Fernandez-Torras, Adrià

AU - Gyori, Benjamin M.

AU - Hartung, Michael

AU - Hoyt, Charles Tapley

AU - Klein, Christoph

AU - Korcsmaros, Tamas

AU - Maier, Andreas

AU - Mann, Matthias

AU - Ochoa, David

AU - Pareja-Lorente, Elena

AU - Popp, Ferdinand

AU - Preusse, Martin

AU - Probul, Niklas

AU - Schwikowski, Benno

AU - Sen, Bünyamin

AU - Strauss, Maximilian T.

AU - Turei, Denes

AU - Ulusoy, Erva

AU - Waltemath, Dagmar

AU - Wodke, Judith A.H.

AU - Saez-Rodriguez, Julio

N1 - Funding Information: This project has received funding from the European Union’s Horizon 2020 research and innovation programme (grant agreement No 965193 (DECIDER) and 116030 (TransQST)), the German Federal Ministry of Education and Research (BMBF, Computational Life Sciences grant No 031L0181B and MSCoreSys research initiative research core SMART-CARE 031L0212A), the US Defense Advanced Research Projects Agency (DARPA) Young Faculty Award (W911NF-20-1-0255), and the Medical Informatics Initiative Germany, MIRACUM consortium (FKZ: 01ZZ2019). We thank Henning Hermjakob, Benjamin Haibe-Kains, Pablo Rodriguez-Mier, Daniel Dimitrov and Olga Ivanova for feedback on the manuscript and Ben Hitz and Pedro Assis for feedback on their use of BioCypher. Funding Information: This project has received funding from the European Union’s Horizon 2020 research and innovation programme (grant agreement No 965193 (DECIDER) and 116030 (TransQST)), the German Federal Ministry of Education and Research (BMBF, Computational Life Sciences grant No 031L0181B and MSCoreSys research initiative research core SMART-CARE 031L0212A), the US Defense Advanced Research Projects Agency (DARPA) Young Faculty Award (W911NF-20-1-0255), and the Medical Informatics Initiative Germany, MIRACUM consortium (FKZ: 01ZZ2019). We thank Henning Hermjakob, Benjamin Haibe-Kains, Pablo Rodriguez-Mier, Daniel Dimitrov and Olga Ivanova for feedback on the manuscript and Ben Hitz and Pedro Assis for feedback on their use of BioCypher.

PY - 2023/8

Y1 - 2023/8

UR - https://www.scopus.com/pages/publications/85162101723

U2 - 10.1038/s41587-023-01848-y

DO - 10.1038/s41587-023-01848-y

M3 - Letter

AN - SCOPUS:85162101723

SN - 1087-0156

VL - 41

SP - 1056

EP - 1059

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 8

ER -

Democratizing knowledge representation with BioCypher

Access to Document

Other files and links

Cite this