Collaborative Research: ABI Innovation: Rapid prototyping of semantic enhancements to biodiversity informatics platforms

合作研究：ABI 创新：生物多样性信息学平台语义增强的快速原型设计

• 批准号: 1356515
• 负责人: Matthew Yoder
• 金额: $ 42.12万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-15 至 2018-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1356515&HistoricalAwards=false
• 关键词: Collaborative; Research; ABI; Innovation; Rapid

This research aims to help scientists develop and use relatively simple tools to describe species in a way that makes those descriptions easier to share with other scientists and easier for computers to process and analyze. Taxonomists are scientists who describe the world's biodiversity. Taxonomists' descriptions of millions of species allow scientists to do many different kinds of research, including basic biology, environmental science, climate research, agriculture, and medicine. The problem is that describing any one species is not easy. The language used by taxonomists to describe their data is complex, and typically not easily understandable by computers nor even other scientists. This situation makes it difficult to search for patterns across the millions of species that have been documented by thousands of different researchers over many decades of work worldwide. Innovation from this project is applicable to the long-term development of open source software initiatives serving laboratories throughout the world, and the research facilitates the production of open, shared data, as mandated by various federal agencies. As a result of this project, these data will become more accessible and informative to the general public. The project provides rich, real-world training for graduate students in library and information sciences, training them to be cross-disciplinary researchers in a field that is in need of new experts. Collaborating experts studying bees, wasps, and ants will receive training on the cutting edge theories and methods from the bioinformatics toolbox developed as a consequence of this project. In return their contributions of data will act as the basis for computational benchmarks needed in areas of logical inference and data modeling.This research addresses the problem of how to produce and utilize semantic data, specifically semantic phenotypes, within the taxonomic context of describing the Earth's biological diversity. The approach to be taken is bottom-up and iterative, involving the rapid prototyping of tools, combining of existing tools, and the tailoring of applications developed for one purpose but now being reused for this scientific activity. Scientists are busy innovating partial solutions by tinkering with and combining available computer programs and datasets. Their efforts comprise an incredibly productive source of innovation, since it is often much easier and faster to combine computer resources that already exist than to build something from scratch. However such cobbling together of resources to meet a need can benefit from analysis and active support. In particular, a more principled set of approaches can make innovations easier to share and to maintain. With a focus on the Hymenoptera, the researchers plan an innovative approach for biodiversity informatics based on work in the field of Computer Supported Cooperative Work (CSCW). Using a combination of ethnography to define work practice, user-centered design, and iterative agile software development, the collaboration between information scientists, biologists, and application developers aims to produce a suite of concrete deliverables, a rapid prototype portfolio, comprising interface and workflow tools, and end user requirements for semantic phenotype production. The project will explore and document examples of innovative prototyping of solutions by scientists to understand how it occurs, what it is that scientists most need, and how these can be most effectively supported. These components may be generalized to allow broader scientific use.

这项研究旨在帮助科学家开发和使用相对简单的工具来描述物种，从而使这些描述更容易与其他科学家共享，并且更容易使计算机处理和分析。分类学家是描述世界生物多样性的科学家。分类学家对数百万种物种的描述使科学家可以进行许多不同的研究，包括基本生物学，环境科学，气候研究，农业和医学。问题是描述任何一种物种都不容易。分类学家用来描述其数据的语言很复杂，通常不容易被计算机或其他科学家理解。这种情况使得很难在全球数十年的工作中搜索数百万个物种的模式。 该项目的创新适用于为全球提供实验室的开源软件计划的长期开发，并且该研究促进了各种联邦机构要求的开放，共享数据的生产。由于该项目，这些数据将变得更加易于访问和信息。该项目为图书馆和信息科学领域的研究生提供了丰富的现实培训，培训它们是需要新专家的领域的跨学科研究人员。研究蜜蜂，黄蜂和蚂蚁的专家合作将接受有关该项目而开发的生物信息学工具箱的最前沿理论和方法的培训。作为回报，他们的数据贡献将充当逻辑推理和数据建模领域所需的计算基准的基础。本研究解决了如何在描述地球生物学多样性的分类学背景下如何生成和利用语义数据，特别是语义表型的问题。要采用的方法是自下而上且迭代的，涉及工具的快速原型制作，现有工具的结合以及为一个目的开发的应用程序的剪裁，但现在被重新用于这项科学活动。科学家正在忙于通过修补并结合可用的计算机程序和数据集来创新部分解决方案。他们的努力包括一个令人难以置信的创新来源，因为相结合已经存在的计算机资源通常比从头开始构建某些东西要容易得多，更快。但是，这样的资源融合在一起可以满足需求，可以从分析和积极支持中受益。特别是，更有原则的方法可以使创新更容易共享和维护。研究人员着重于膜翅目，根据计算机支持合作工作（CSCW）的工作计划了一种创新的生物多样性信息学方法。通过民族志的结合来定义工作实践，以用户为中心的设计和迭代敏捷软件开发，信息科学家，生物学家和应用程序开发人员之间的协作旨在生产一套混凝土可交付成果，这是一种快速的原型投资组合，构成界面和工作流程的快速原型组合，以及对Semantic tymantype型生产的最终用户需求。该项目将探索和记录科学家对解决方案创新原型制作的例子，以了解其发生的方式，科学家最需要的是什么以及如何得到最有效的支持。这些组件可能会被推广，以允许更广泛的科学用途。