一个简单的本体映射共享标准（SSSOM）

SSSOM是一个简单的本体映射共享标准，提供

1. 基于TSV的本体术语映射表示
2. 一套完整的标准元数据元素来描述映射
3. TSV和Web本体语言（OWL）之间的标准翻译。

特别是，SSSOM的TSV格式旨在满足更广泛的生物信息学社区的需求，作为一种以易于阅读且语义良好指定的方式安全交换映射的方法。以下是一个简单的映射文件示例

SSSOM指定了所有其元数据元素

• 主题_id
• 谓词_id
• 对象_id
• 映射依据（注意：自2022年6月起 match_type 正被 mapping_justification 替换，详见 此处）
• 主题标签
• 对象标签

包括清晰的定义、使用示例以及必要时控制的词汇，以及30个其他可选的元数据元素，以提供额外的来源。

SSSOM还提供了一个标准方法来

• 通过映射集级别的元数据（如 creator_id、mapping_date 或许可）增强TSV文件，并将
• SSSOM兼容的TSV文件转换为 OWL 实体化公理。这将允许使用标准工具（如 ROBOT，正在开发中）轻松加载和合并 SSSOM 映射表到现有本体。

请注意，SSSOM 目前处于开发中，可能发生变化。如果您想参与其中，请在 问题跟踪器 上留下评论。完整规范可在 此处 找到。

引用

如果您在您的工作中发现 SSSOM 有帮助，请考虑引用

Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A McLaughlin, Julie A McMurry, Sierra Moxon, Monica C Munoz-Torres, David Osumi-Sutherland, James A Overton, Bjoern Peters, Tim Putman, Núria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H Wagner, Christopher J Mungall, A Simple Standard for Sharing Ontological Mappings (SSSOM), Database, Volume 2022, 2022, baac035, https://doi.org/10.1093/database/baac035

@article{10.1093/database/baac035,
    author = {Matentzoglu, Nicolas and Balhoff, James P and Bello, Susan M and Bizon, Chris and Brush, Matthew and Callahan, Tiffany J and Chute, Christopher G and Duncan, William D and Evelo, Chris T and Gabriel, Davera and Graybeal, John and Gray, Alasdair and Gyori, Benjamin M and Haendel, Melissa and Harmse, Henriette and Harris, Nomi L and Harrow, Ian and Hegde, Harshad B and Hoyt, Amelia L and Hoyt, Charles T and Jiao, Dazhi and Jiménez-Ruiz, Ernesto and Jupp, Simon and Kim, Hyeongsik and Koehler, Sebastian and Liener, Thomas and Long, Qinqin and Malone, James and McLaughlin, James A and McMurry, Julie A and Moxon, Sierra and Munoz-Torres, Monica C and Osumi-Sutherland, David and Overton, James A and Peters, Bjoern and Putman, Tim and Queralt-Rosinach, Núria and Shefchek, Kent and Solbrig, Harold and Thessen, Anne and Tudorache, Tania and Vasilevsky, Nicole and Wagner, Alex H and Mungall, Christopher J},
    title = "{A Simple Standard for Sharing Ontological Mappings (SSSOM)}",
    journal = {Database},
    volume = {2022},
    year = {2022},
    month = {05},
    abstract = "{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}",
    issn = {1758-0463},
    doi = {10.1093/database/baac035},
    url = {https://doi.org/10.1093/database/baac035},
    note = {baac035},
    eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac035/43832024/baac035.pdf},
}

自上述主要 SSSOM 公布以来，发布了包含更新的 第二份报告，作为 2022 年本体匹配研讨会的一部分。

复制

SSSOM 根据 3-clause BSD 许可证的条款进行分发，如源分发中的 LICENSE 文件中所述。

例外情况下，以下文件不适用 3-clause BSD 许可证

• sssom-banner.png：该文件仅可用于内部 Monarch 团队成员和 Monarch 标志性产品的合作者。