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以适当地存储，但协议本身往往只记录在纸面上，或者作为为执行协议而开发的脚本以电子方式存储。一旦实施该方案的科学家离开实验室，这一记录可能就会丢失。收集的数据集在没有描述用于产生它们的过程的情况下变得毫无意义；此外，为产生数据而设计的实验是不可重复的。这项研究正在开发一个数据库(ProtocolDB)来管理科学方案和从执行方案中收集到的数据集。这种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。这项研究还解决了记录和查询数据来源(为什么和在哪里)的问题。ProtocolDB将使科学家受益，因为它为实验室提供了一个科学档案，它不仅能够查询和推理协议、协议的执行和收集的数据集，而且能够实现团队之间的数据共享和协作。研究的智力价值包括设计科学工作流模型，以及用于检索、转换、比较科学工作流、集成数据集和关于数据来源的推理的查询语言。这一理论贡献将在支持科学协议表达的系统开发方面取得进展。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的影响是开发了一个管理科学方案及其收集的数据集的通用系统。包括学术机构、政府机构和私人机构在内的已建立的合作将极大地促进其使用的广度。

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.