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

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，使这些描述更容易与其他科学家分享，也更容易被计算机处理和分析。分类学家是描述世界生物多样性的科学家。分类学家对数以百万计的物种的描述允许科学家进行许多不同类型的研究，包括基础生物学、环境科学、气候研究、农业和医学。问题是，描述任何一个物种都不容易。分类学家用来描述他们的数据的语言很复杂，通常计算机甚至其他科学家都不容易理解。这种情况使得在全世界数千名不同研究人员数十年的工作中记录的数百万个物种中搜索模式变得困难。该项目的创新适用于为世界各地的实验室服务的开放源码软件倡议的长期开发，并且该研究促进了开放、共享数据的产生，正如各联邦机构所要求的那样。这一项目的结果是，这些数据将变得更容易获得，并为公众提供更多信息。该项目为图书馆学和情报学的研究生提供丰富的现实世界培训，培训他们成为一个需要新专家的领域的跨学科研究人员。研究蜜蜂、黄蜂和蚂蚁的合作专家将从作为该项目结果而开发的生物信息学工具箱中接受关于尖端理论和方法的培训。作为回报，他们对数据的贡献将作为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多样性的分类背景下产生和利用语义数据，特别是语义表型的问题。将采取的方法是自下而上和迭代的，包括工具的快速原型设计、现有工具的组合以及为一个目的开发的但现在被重复用于这一科学活动的应用程序的定制。科学家们正忙于通过修补和组合现有的计算机程序和数据集来创新部分解决方案。他们的努力构成了一个令人难以置信的多产的创新来源，因为整合现有的计算机资源往往比从头开始构建要容易得多，也更快。然而，这种为满足需求而拼凑资源的做法可以从分析和积极支持中受益。特别是，一套更有原则的方法可以使创新更容易分享和维护。以膜翅目为重点，研究人员在计算机支持的协同工作(CSCW)领域的工作基础上，计划了一种创新的生物多样性信息学方法。使用人种志的组合来定义工作实践、以用户为中心的设计和迭代的敏捷软件开发，信息科学家、生物学家和应用程序开发人员之间的合作旨在产生一套具体的可交付成果、快速原型组合，包括界面和工作流工具，以及最终用户对语义表型生产的需求。该项目将探索和记录科学家创新解决方案原型的例子，以了解它是如何发生的，科学家最需要的是什么，以及如何才能最有效地支持这些问题。这些成分可以被推广，以允许更广泛的科学用途。

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.