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

该项目正在解决科学研究中的一个系统性问题：虽然通过科学协议收集的数据集可能会得到适当的存储，但协议本身往往只记录在纸上或以电子方式存储为执行协议而开发的脚本。一旦实施该方案的科学家离开实验室，该记录可能会丢失。如果没有对产生数据的过程的描述，收集的数据集就变得毫无意义;此外，设计用于产生数据的实验是不可重复的。该研究正在开发一个数据库（ProtocolDB），用于管理科学协议及其执行过程中收集的数据集。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。这项研究还涉及记录和查询数据来源（原因和地点）的问题。ProtocolDB将通过为实验室提供科学组合来使科学家受益，不仅可以查询和推理协议，执行协议和收集的数据集，还可以实现团队之间的数据共享和协作。该研究的智力价值包括科学工作流模型的设计，以及用于检索、转换、比较科学工作流、集成数据集和推理数据来源的查询语言。这一理论贡献将建立支持科学协议表达的系统的发展的进步。ProtocolDB的实施将由我们的科学合作伙伴进行评估。该项目产生的更广泛影响是开发了一个管理科学协议及其收集的数据集的通用系统。已建立的合作，涉及学术，政府和私人机构，将大大有助于其使用的广度。

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.