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 。
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, Paul Clemons, Vlado Dancik, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, ... >>>
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, Paul Clemons, Vlado Dancik, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne T. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall, the Biomedical Data Translator Consortium <<<
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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