Collaborative Research: SEI+II ProtocolDB: Archiving and Querying Scientific Protocols, Data and Provenance

合作研究：SEI II ProtocolDB：归档和查询科学协议、数据和来源

• 批准号: 0612177
• 负责人: Susan Davidson
• 金额: $ 22万
• 依托单位: University of Pennsylvania
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-15 至 2009-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0612177&HistoricalAwards=false
• 关键词: Collaborative; Research; SEI+II; ProtocolDB; Archiving

This project is addressing a systemic problem in scientific research: although datasets collected through scientific protocols may be properly stored, the protocol itself is often only recorded on paper or stored electronically as the script developed to implement the protocol. Once the scientist who has implemented the protocol leaves the laboratory, this record may be lost. Collected datasets become meaningless without a description of the process used to produce them; furthermore, the experiment designed to produce the data is not reproducible. This research is developing a database (ProtocolDB) to manage scientific protocols and the collected datasets obtained from their execution. The approach will allow scientists to query, compare and revise protocols, and express queries across protocols and data. The research is also addressing the issue of recording and querying the provenance (the why and where) of data. ProtocolDB will benefit scientists by providing a scientific portfolio for the laboratory which not only enables querying and reasoning about protocols, executions of protocols and collected datasets, but enables data sharing and collaborations between teams. The intellectual merit of the research includes the design of a model for scientific workflows, and a query language to retrieve, transform, compare scientific workflows, integrate datasets, and reason about data provenance. This theoretical contribution will establish advances in the development of systems supporting the expression of scientific protocols. The ProtocolDB implementation will be evaluated by our scientific partners. The broader impact resulting from the project is the development of a general-purpose system for managing scientific protocols and their collected datasets. The established collaborations, involving academic, governmental, and private institutions, will contribute significantly to the breadth of its use.

该项目正在解决科学研究中的系统问题：尽管可以正确存储通过科学协议收集的数据集，但该协议本身通常仅在纸上记录在纸上或以电子方式记录在电子上，因为脚本为实施协议而开发。一旦实施该协议的科学家就会离开实验室，这一记录可能会丢失。收集的数据集变得毫无意义，而没有描述用于生产它们的过程的描述；此外，设计用于生成数据的实验是不可再现的。这项研究正在开发一个数据库（ProtoColdB）来管理科学协议和从其执行中获得的收集数据集。该方法将允许科学家查询，比较和修改协议，并跨协议和数据表达查询。该研究还解决了记录和查询数据的出处（原因和地点）的问题。 ProtoColdB将通过为实验室提供科学投资组合来使科学家受益，该实验室不仅可以对协议，协议执行和收集的数据集进行查询和推理，而且还可以实现团队之间的数据共享和协作。该研究的智力优点包括设计用于科学工作流的模型，以及用于检索，转换，比较科学工作流，整合数据集的查询语言以及有关数据出处的原因。这种理论上的贡献将在支持科学协议表达的系统的发展方面建立进步。 ProtoColdB实施将由我们的科学伙伴评估。该项目产生的更广泛的影响是开发用于管理科学协议及其收集数据集的通用系统。涉及学术，政府和私人机构的既定合作将对其使用的广度做出重大贡献。