脊椎动物品种本体论：迈向有效的品种数据标准化

The Vertebrate Breed Ontology: Towards effective breed data standardization.

作者信息

Mullen Kathleen R, Tammen Imke, Matentzoglu Nicolas A, Mather Marius, Balhoff James P, Esdaile Elizabeth, Leroy Gregoire, Park Carissa A, Rando Halie M, Saklou Nadia T, Webb Tracy L, Vasilevsky Nicole A, Mungall Christopher J, Haendel Melissa A, Nicholas Frank W, Toro Sabrina

机构信息

Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia.

出版信息

ArXiv. 2025 Jan 24:arXiv:2406.02623v2.

PMID:38883236

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11177956/

Abstract

BACKGROUND –: Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the application of existing information-based tools to support advancement in diagnostics, treatments, and precision medicine.

HYPOTHESIS/OBJECTIVES –: A single, coherent, logic-based standard for documenting breed names in health, production, and research-related records will improve data use capabilities in veterinary and comparative medicine.

ANIMALS –: No live animals were used.

METHODS –: The Vertebrate Breed Ontology (VBO) was created from breed names and related information compiled from the Food and Agriculture Organization of the United Nations, breed registries, communities, and experts, using manual and computational approaches. Each breed is represented by a VBO term that includes breed information and provenance as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence-readiness.

RESULTS –: VBO is an open, community-driven ontology representing over 19,500 livestock and companion animal breed concepts covering 49 species. Breeds are classified based on community and expert conventions (e.g., cattle breed) and supported by relations to the breed's genus and species indicated by National Center for Biotechnology Information (NCBI) Taxonomy terms. Relationships between VBO terms (e.g., relating breeds to their foundation stock) provide additional context to support advanced data analytics. VBO term metadata includes synonyms, breed identifiers/codes, and attributed cross-references to other databases.

CONCLUSION AND CLINICAL IMPORTANCE –: The adoption of VBO as a source of standard breed names in databases and veterinary electronic health records can enhance veterinary data interoperability and computability.

摘要

背景

兽医学中普遍采用的数据标准有限，这阻碍了数据的互操作性，进而影响了数据的整合与比较；这最终阻碍了现有基于信息的工具在诊断、治疗和精准医学进步方面的应用。

假设/目标：制定一个单一、连贯、基于逻辑的标准，用于在健康、生产和研究相关记录中记录品种名称，将提高兽医和比较医学中的数据使用能力。

动物

未使用活体动物。

方法

脊椎动物品种本体（VBO）是通过手动和计算方法，从联合国粮食及农业组织、品种登记处、社区和专家汇编的品种名称及相关信息中创建的。每个品种由一个VBO术语表示，该术语包括品种信息和来源作为元数据。VBO术语使用描述逻辑进行分类，以实现计算应用和人工智能兼容性。

结果

VBO是一个开放的、由社区驱动的本体，代表了超过19500个家畜和伴侣动物品种概念，涵盖49个物种。品种根据社区和专家惯例进行分类（如牛品种），并由与国家生物技术信息中心（NCBI）分类术语所指示的品种属和种的关系提供支持。VBO术语之间的关系（如将品种与其基础种群相关联）提供了额外的背景信息，以支持高级数据分析。VBO术语元数据包括同义词、品种标识符/代码以及对其他数据库的归因交叉引用。