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招聘:公平分类概念表示及关系的标准。

Wanted: Standards for FAIR taxonomic concept representations and relationships.

作者信息

Sterner Beckett, Upham Nathan, Gupta Prashant, Powell Caleb, Franz Nico M

机构信息

Arizona State University, Tempe, United States of America.

出版信息

Biodivers Inf Sci Stand. 2021;5. doi: 10.3897/biss.5.75587. Epub 2021 Sep 23.

DOI:10.3897/biss.5.75587
PMID:35462676
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9028594/
Abstract

Making the most of biodiversity data requires linking observations of biological species from multiple sources both efficiently and accurately (Bisby 2000, Franz et al. 2016). Aggregating occurrence records using taxonomic names and synonyms is computationally efficient but known to experience significant limitations on accuracy when the assumption of one-to-one relationships between names and biological entities breaks down (Remsen 2016, Franz and Sterner 2018). Taxonomic treatments and checklists provide authoritative information about the correct usage of names for species, including operational representations of the meanings of those names in the form of range maps, reference genetic sequences, or diagnostic traits. They increasingly provide taxonomic intelligence in the form of precise description of the semantic relationships between different published names in the literature. Making this authoritative information Findable, Accessible, Interoperable, and Reusable (FAIR; Wilkinson et al. 2016) would be a transformative advance for biodiversity data sharing and help drive adoption and novel extensions of existing standards such as the Taxonomic Concept Schema and the OpenBiodiv Ontology (Kennedy et al. 2006, Senderov et al. 2018). We call for the greater, global Biodiversity Information Standards (TDWG) and taxonomy community to commit to on how FAIR applies to biodiversity data and include practical targets and criteria for the publication and digitization of taxonomic concept representations and alignments in taxonomic treatments, checklists, and backbones.

摘要

充分利用生物多样性数据需要高效且准确地将来自多个来源的生物物种观测数据联系起来(比兹比,2000年;弗兰兹等人,2016年)。使用分类学名称和同义词汇总出现记录在计算上是高效的,但当名称与生物实体之间一对一关系的假设不成立时,已知在准确性方面会有显著限制(雷姆森,2016年;弗兰兹和施特纳尔,2018年)。分类学处理和名录提供了关于物种名称正确用法的权威信息,包括以分布图、参考基因序列或诊断特征等形式呈现的这些名称含义的操作表示。它们越来越多地以精确描述文献中不同已发表名称之间语义关系的形式提供分类学知识。使这些权威信息具有可查找、可访问、可互操作和可重用性(FAIR;威尔金森等人,2016年)将是生物多样性数据共享的变革性进展,并有助于推动采用和扩展现有标准,如分类学概念模式和开放生物多样性本体(肯尼迪等人,2006年;森德罗夫等人,2018年)。我们呼吁全球更大的生物多样性信息标准(TDWG)和分类学界致力于研究FAIR如何应用于生物多样性数据,并纳入分类学概念表示以及分类学处理、名录和主干中的比对的发布和数字化的实际目标及标准。

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1
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2
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J Biomed Semantics. 2018 Jan 18;9(1):5. doi: 10.1186/s13326-017-0174-5.
3
To increase trust, change the social design behind aggregated biodiversity data.为了增加信任,改变聚合生物多样性数据背后的社会设计。
Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bax100.
4
Two Influential Primate Classifications Logically Aligned.两种有影响力的灵长类动物分类在逻辑上保持一致。
Syst Biol. 2016 Jul;65(4):561-82. doi: 10.1093/sysbio/syw023. Epub 2016 Mar 22.
5
The FAIR Guiding Principles for scientific data management and stewardship.科学数据管理和保存的 FAIR 指导原则。
Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18.
6
The use and limits of scientific names in biological informatics.生物信息学中科学名称的使用与局限
Zookeys. 2016 Jan 7(550):207-23. doi: 10.3897/zookeys.550.9546. eCollection 2016.
7
Standard data model representation for taxonomic information.分类信息的标准数据模型表示。
OMICS. 2006 Summer;10(2):220-30. doi: 10.1089/omi.2006.10.220.
8
Microsatellite variation and evolution in the Peromyscus maniculatus species group.鹿鼠物种组中的微卫星变异与进化。
Mol Phylogenet Evol. 2005 Feb;34(2):408-15. doi: 10.1016/j.ympev.2004.10.018. Epub 2004 Dec 15.
9
The quiet revolution: biodiversity informatics and the internet.悄然兴起的革命:生物多样性信息学与互联网
Science. 2000 Sep 29;289(5488):2309-12. doi: 10.1126/science.289.5488.2309.