Automation of Natural History Collections and Bioinformatics: Rapid Optical Data Acquisition and Automated Computerization at INHS

自然历史收藏和生物信息学的自动化：INHS 的快速光学数据采集和自动计算机化

• 批准号: 1132188
• 负责人: Paul Tinerella
• 金额: $ 26.85万
• 依托单位: University of Minnesota-Twin Cities
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-12-01 至 2013-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1132188&HistoricalAwards=false
• 关键词: Automation; Natural; History; Collections; Bioinformatics

This project will digitize and computerize approximately 489,000 specimens of Collembola (springtails), Thysanoptera (thrips), Phthiraptera (lice), and Psocoptera (book and bark lice) into a rapid data acquisition imaging/database workflow recently developed in the entomology collections at the Illinois Natural History Survey. Digitization and computerization will be achieved by optical scanning of glass slide preparations and collection labels from ethanol-preserved material (vials). Upon batch scanning, programming language scripts will be used to a) automate capture of each collection object image into the database as an individual specimen record; and b) semi-automate data entry into relational database fields. The first pass of semi-automated parsing of specimen data results in an average of 60% of the complete individual record automatically parsed into the database. A second pass using computer scripts and interactive data entry, recovers the remaining collection object data. An important contribution of this proposed natural history collections digitization solution is the implementation of a database/software workflow that allows integration of verbatim label data (imaged) with the traditional specimen-level database. This newly developed imaging/database solution will transform the way, and accurately accelerate the rate, in which invaluable natural history collections are digitized. The workflow will be integrated with the NSF-supported Specify collections management software and be made available for broader use in the natural history collections community. Application of this workflow solution will facilitate complete curation for the groups of INHS insects listed, making available a wealth of critical historical and modern-day collections data to researchers and the public, worldwide. The project will provide training for two graduate students, one database technician, and select undergraduates in biodiversity informatics. Availability of this solution will benefit the greater biological collections community with efforts to rapidly digitize, integrate, and mobilize collections data. This project is part of a 10-year effort to digitize and mobilize the scientific information associated with biological specimens held in U.S. research collections. The images and digitized data from this project will be integrated into the online national resource as outlined in the community strategic plan available at http://digbiocol.files.wordpress.com/2010/05/digistratplanfinaldraft.pdf.

该项目将把大约489,000个弹尾目(弹尾目)、胸翅目(蓟马)、跳蚤目(虱子)和后翅目(书虱和树皮虱)标本数字化和计算机化，成为伊利诺伊州自然历史调查局昆虫学收藏品中最近开发的快速数据采集成像/数据库工作流。数字化和计算机化将通过光学扫描玻璃片制剂和乙醇保存材料(瓶子)的收集标签来实现。在批量扫描时，编程语言脚本将用于a)将每个收集对象图像作为单独的标本记录自动捕获到数据库中；以及b)将数据半自动输入到关系数据库字段中。标本数据的第一次半自动解析导致平均60%的完整个体记录被自动解析到数据库中。使用计算机脚本和交互式数据输入的第二遍恢复剩余的收集对象数据。这一拟议的自然历史收藏数字化解决方案的一个重要贡献是实施了一个数据库/软件工作流程，允许将逐字标签数据(图像)与传统标本级别的数据库相结合。这一新开发的成像/数据库解决方案将改变方式，并准确地加快宝贵的自然历史收藏数字化的速度。该工作流程将与NSF支持的指定收藏管理软件集成，并在自然历史收藏社区中提供更广泛的使用。这一工作流程解决方案的应用将有助于对列出的INHS昆虫组进行完整的管理，向世界各地的研究人员和公众提供大量重要的历史和现代收集数据。该项目将为两名研究生、一名数据库技术员提供培训，并挑选生物多样性信息学方面的本科生。这一解决方案的提供将使更多的生物收藏界受益，努力实现收藏品数据的快速数字化、整合和移动。该项目是一项为期10年的努力的一部分，目的是将与美国研究藏品中的生物标本相关的科学信息数字化和移动化。该项目的图像和数字化数据将整合到在线国家资源中，如可在http://digbiocol.files.wordpress.com/2010/05/digistratplanfinaldraft.pdf.获得的社区战略计划中所述