论文标题
用生物透明的知识代表民主化
Democratising Knowledge Representation with BioCypher
论文作者
论文摘要
在所有研究人员中标准化生物医学知识的表示是一项无法克服的任务，阻碍了许多计算方法的有效性。尽管有这一基本挑战，但我们提出促进协调和互操作性，我们建议将知识图创建的框架标准化。我们在BioCypher中实施了这种标准化，这是一个公平的（可访问，可互操作，可重复使用的）框架，以透明地构建生物医学知识图，同时保留源数据的证明。将知识映射到生物医学本体上，有助于平衡对非专业研究人员的协调，人类和机器可读性以及易用性和可访问性的需求。我们证明了该框架对各种用例的有用性，从特定于任务的知识商店的维护到生物医学领域之间的互操作性，再到为联合学习的需求建立特定于任务的知识图。 BioCypher（https://biocypher.org）释放了宝贵的开发人员时间；我们鼓励社区进一步发展和使用。
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 this 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) frees up valuable developer time; we encourage further development and usage by the community.
