小W
(2024-02-29 20:28):
#paper doi:arXiv:2203.13906 Biolink Model: A Universal Schema for Knowledge Graphs in
Clinical, Biomedical, and Translational Science 本文介绍了欧洲分子生物学实验室对于生命进程的认识 Biolink 模型,其使用yaml变体 linkml ( Linked data Modeling Language )定义一组分层的、相互关联的类以及它们之间的关系,以此来表征转化科学中的实体以及这些实体之间的联系。其工作包含标准生物模式、样本、TranslatorMinimal三个模型库以及使用其模型关联不同本体数据的方法。基于此模型,其他团队开发了NIH 的Biomedical Data Translator项目,以及 2023 发表于 Nat. Biotechnol 的 BioCypher 。
arXiv,
2022.
DOI: 10.48550/arXiv.2203.13906
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science
Abstract:
Within clinical, biomedical, and translational science, an increasing number<br>of projects are adopting graphs for knowledge representation. Graph-based data<br>models elucidate the interconnectedness between core biomedical concepts,<br>enable data structures to be easily updated, and support intuitive queries,<br>visualizations, and inference algorithms. However, knowledge discovery across<br>these "knowledge graphs" (KGs) has remained difficult. Data set heterogeneity<br>and complexity; the proliferation of ad hoc data formats; poor compliance with<br>guidelines on findability, accessibility, interoperability, and reusability;<br>and, in particular, the lack of a universally-accepted, open-access model for<br>standardization across biomedical KGs has left the task of reconciling data<br>sources to downstream consumers. Biolink Model is an open source data model<br>that can be used to formalize the relationships between data structures in<br>translational science. It incorporates object-oriented classification and<br>graph-oriented features. The core of the model is a set of hierarchical,<br>interconnected classes (or categories) and relationships between them (or<br>predicates), representing biomedical entities such as gene, disease, chemical,<br>anatomical structure, and phenotype. The model provides class and edge<br>attributes and associations that guide how entities should relate to one<br>another. Here, we highlight the need for a standardized data model for KGs,<br>describe Biolink Model, and compare it with other models. We demonstrate the<br>utility of Biolink Model in various initiatives, including the Biomedical Data<br>Translator Consortium and the Monarch Initiative, and show how it has supported<br>easier integration and interoperability of biomedical KGs, bringing together<br>knowledge from multiple sources and helping to realize the goals of<br>translational science.
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