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Pré-Publication, Document De Travail (Preprint/Prepublication) Année : 2023

Democratizing knowledge representation with BioCypher

Jan Baumbach
Adrià Fernandez-Torras
  • Fonction : Auteur
Benjamin Gyori
Michael Hartung
Charles Tapley Hoyt
  • Fonction : Auteur
David Ochoa
Elena Pareja-Lorente
  • Fonction : Auteur
Niklas Probul
Bünyamin Sen
Maximilian Strauss
Denes Turei
  • Fonction : Auteur
Erva Ulusoy

Résumé

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to non-specialist researchers. We demonstrate the usefulness of the framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://biocypher.org) thus facilitates automating knowledge-based biomedical research, and we encourage the community to further develop and use it.
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Licence : CC BY - Paternité

Dates et versions

hal-04135813 , version 1 (28-06-2023)

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Paternité

Identifiants

  • HAL Id : hal-04135813 , version 1

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Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar, Pornpimol Charoentong, et al.. Democratizing knowledge representation with BioCypher. 2023. ⟨hal-04135813⟩
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