Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.
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DOI：
10.1111/cts.13302
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发表时间：
2022-08
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影响因子：
--
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中科院分区：
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在临床、生物医学和翻译科学中，越来越多的项目正在采用图形来表示知识。基于图的数据模型阐明了核心生物医学概念之间的相互联系，使数据结构易于更新，并支持直观的查询、可视化和推理算法。然而，跨越这些“知识图谱”(KG)的知识发现仍然很困难。数据集的异质性和复杂性；特别数据格式的激增；对关于可发现性、可访问性、互操作性和可重用性的指导方针的遵从性差；尤其是，缺乏一个普遍接受的、开放获取的跨生物医学KG标准化模式，这使得将数据源协调给下游消费者的任务变得更加艰巨。Biolink模型是一种开源数据模型，可用于在翻译科学中形式化数据结构之间的关系。它结合了面向对象的分类和面向图形的功能。该模型的核心是一组层次化的、相互关联的类(或类别)以及它们(或谓词)之间的关系，表示生物医学实体，如基因、疾病、化学、解剖结构和表型。该模型提供了类和边属性以及关联，这些属性和关联指导实体应该如何相互关联。这里，我们强调了为KGS建立标准化数据模型的必要性，描述了Biolink模型，并将其与其他模型进行了比较。我们展示了Biolink模型在各种倡议中的效用，包括生物医学数据翻译者联盟和君主倡议，并展示了它如何支持生物医学KG更容易的集成和互操作性，汇集来自多个来源的知识，并帮助实现翻译科学的目标。
Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.
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影响因子：
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作者：
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通讯作者：
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DOI：
10.1016/j.patter.2020.100155
发表时间：
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期刊：
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发表时间：
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期刊：
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影响因子：
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