ABI Innovation: Authors in the driver's seat: fast, consistent, computable phenotype data and ontology production

ABI 创新：作者主导：快速、一致、可计算的表型数据和本体生成

• 批准号: 1661485
• 负责人: Hong Cui
• 金额: $ 64.18万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-07-01 至 2022-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661485&HistoricalAwards=false
• 关键词: ABI; Innovation; Authors; driver; seat

Modern evolutionary research requires organism character data from multiple branches of the Tree of Life, but the majority of such data are in a "legacy" format that computers can not use. Highly trained postdoc scientists are employed to manually convert them. By one estimate, one year's worth of English biomedical journal publications alone would take a full-time postdoc over 30 years to convert. This manual process is fundamentally problematics for three reasons: First, it does not stop the continued publication of character descriptions in the legacy format. Second, it takes time away from highly trained scientists and preventing them from making new and more important discoveries. Third, it does not address the fundamental causes of large differences (~ 40%) in the data converted by different scientists, resulting in less useful data. This project will investigate a transformative approach that solves the problem at its root, by enabling authors of biodiversity works to directly produce computable data at the time of publication, eliminating the need for subsequent post-publication data conversion. Scientists will be able to direct use the published data in the new format to address grand conservation, environmental, or medical challenges facing humankind today. This research has great potential to solve the phenotype data production problem at its root. It recognizes that authors make (implicit) ontological commitments when writing a descriptive work and that they are best qualified to interpret the work. Instead of limiting authors to any "standardized" terminology, authors will be provided with a low-barrier, efficient, open-collaboration platform to describe characters as accurately as they wish using an ontology built collectively with other authors working on similar taxa. This process makes authors more aware of term usage in the community and helps the community (including younger generation of scientists) converge on best practices. The result will be that all character terms included in the descriptive work are documented/defined in the taxon-specific ontology and the descriptions are consequently made semantically clear, and ready for software to harvest computable character data. The software platform to be developed by this project exposes disagreements among authors and usage-based term status in the ontology, and notifies authors of updates and conflicts via a mobile-friendly app. Taking into account user motivation and attribution factors, the project will design, implement, and evaluate the approach from both human social behavior and software usability perspectives, employing recent results from open online collaboration research and cutting-edge usability test techniques (e.g., measuring user stress levels via eye-tracking and pupil dilation). The success of the project is generalizable to other domains and will fundamentally change the way phenotypic characters are documented and used in biological research. The results of the project will be found at http://github.com/orgs/biosemantics/projects.

现代进化研究需要来自生命之树多个分支的生物特征数据，但这些数据中的大多数都是“遗留”格式，计算机无法使用。训练有素的博士后科学家被雇用来手工转换它们。据估计，仅一年的英国生物医学期刊出版物就需要一个全职博士后30多年的时间来转换。这个手工过程从根本上说是有问题的，原因有三：首先，它不能阻止以遗留格式继续发布字符描述。其次，它占用了训练有素的科学家的时间，阻碍了他们做出新的、更重要的发现。第三，它没有解决不同科学家转换的数据存在巨大差异（~ 40%）的根本原因，导致数据不太有用。该项目将研究一种从根本上解决问题的变革性方法，使生物多样性作品的作者能够在出版时直接产生可计算的数据，从而消除随后出版后数据转换的需要。科学家将能够直接使用以新格式发布的数据来解决人类今天面临的重大保护、环境或医疗挑战。本研究具有从根本上解决表型数据产生问题的巨大潜力。它承认作者在撰写描述性作品时做出（隐含的）本体论承诺，并且他们最有资格解释作品。而不是限制作者任何“标准化”的术语，作者将提供一个低障碍，高效，开放的协作平台，以准确地描述字符使用本体与其他作者共同建立类似的分类群。这个过程使作者更加了解术语在社区中的使用，并帮助社区（包括年轻一代的科学家）集中在最佳实践上。结果将是，描述性工作中包含的所有字符术语都在特定分类单元的本体中被记录/定义，并且描述因此在语义上变得清晰，并为软件收集可计算的字符数据做好准备。该项目将开发的软件平台将揭示作者之间的分歧和本体中基于使用的术语状态，并通过移动友好的应用程序通知作者更新和冲突。考虑到用户动机和归因因素，该项目将从人类社会行为和软件可用性的角度设计、实施和评估该方法。采用开放在线协作研究和尖端可用性测试技术的最新结果（例如，通过眼球追踪和瞳孔扩张来测量用户的压力水平）。该项目的成功可以推广到其他领域，并将从根本上改变表型特征在生物学研究中的记录和使用方式。该项目的结果可在http://github.com/orgs/biosemantics/projects上找到。

项目成果

Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier

• DOI: 10.3897/bdj.6.e29232
• 发表时间: 2018-11-28
• 期刊: BIODIVERSITY DATA JOURNAL
• 影响因子: 1.3
• 作者: Endara，Lorena;Thessen，Anne E.;Cui，Hong
• 通讯作者: Cui，Hong

Author-Driven Computable Data and Ontology Production for Taxonomists

为分类学家提供作者驱动的可计算数据和本体生产

• DOI: 10.3897/biss.5.75741
• 发表时间: 2021
• 期刊: Biodiversity Information Science and Standards
• 作者: Cui, Hong;Ford, Bruce;Starr, Julian;Macklin, James;Reznicek, Anton;Giebink, Noah;Longert, Dylan;Léveillé-Bourret, Étienne;Zhang, Limin
• 通讯作者: Zhang, Limin

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes.

• DOI: 10.1093/database/baaa079
• 发表时间: 2020-11-20
• 期刊: Database : the journal of biological databases and curation
• 作者: Cui H;Zhang L;Ford B;Cheng HL;Macklin JA;Reznicek A;Starr J
• 通讯作者: Starr J

Preliminary Findings of Usability Studies on an Ontology-Aware Taxon-by-Character Matrix Editor

本体感知分类单元字符矩阵编辑器可用性研究的初步结果

• DOI: 10.3897/biss.6.90949
• 发表时间: 2022
• 期刊: Biodiversity Information Science and Standards
• 作者: Cui, Hong;Ford, Bruce;Starr, Julian;Reznicek, Anton;Zhou, Yuxuan;Gan, Quan;Léveillé-Bourret, Étienne;Lacroix-Carignan, Étienne;Macklin, James;Cayouette, Jacques
• 通讯作者: Cayouette, Jacques