Semanticly Ltd, London WC2H 9JQ, UK.
RENCI, University of North Carolina, Chapel Hill, NC 27517, USA.
Database (Oxford). 2022 May 25;2022. doi: 10.1093/database/baac035.
Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec.
尽管在描述和交换科学信息的标准制定方面取得了进展，但在不同数据库中相同或相似对象的不同表示之间缺乏易于使用的映射标准，这仍然是数据集成和互操作性的主要障碍。映射通常缺乏正确解释和应用所需的元数据。例如，两个术语是等效的还是仅仅相关？它们是窄匹配还是宽匹配？或者它们以其他方式相关联？这些映射术语之间的关系通常没有记录，这导致了不正确的假设，并且在需要高精度的场景（例如诊断或风险预测）中难以使用。此外，由于缺乏对映射方式的描述，使得难以组合和协调映射，特别是经过人工整理和自动化的映射。我们开发了简单的共享本体映射标准（Simple Standard for Sharing Ontological Mappings，SSSOM），通过以下方式解决了这些问题：（i）引入机器可读和可扩展的词汇表来描述元数据，从而明确映射中的不精确性、不准确性和不完整性。（ii）定义一种易于使用的简单基于表格的格式，可以集成到现有的数据科学管道中，而无需解析或查询本体，并且与链接数据原则无缝集成。（iii）实现开放和社区驱动的协作工作流程，旨在不断发展标准，以满足不断变化的要求和映射实践。（iv）提供用于处理标准的参考工具和软件库。在本文中，我们介绍了 SSSOM 标准，详细描述了几个用例，并调查了一些关于标准化映射交换的现有工作，旨在使映射具有可发现性、可访问性、互操作性和可重用性（Findable, Accessible, Interoperable and Reusable，FAIR）。SSSOM 规范可以在 http://w3id.org/sssom/spec 找到。数据库地址：http://w3id.org/sssom/spec。
