Science is increasingly data-driven. Scientific research funders now routinely mandate open publication of publicly-funded research data. Safely reusing such data currently requires labour-intensive curation. Provenance recording the history and derivation of the data is critical to reaping the benefits and avoiding the pitfalls of data sharing. There are hundreds of curated scientific databases in biomedicine that need fine-grained provenance; one important example is the IUPHAR/BPS Guide to Pharmacology database (GtoPdb), a pharmacological database developed in Edinburgh.
Currently there are no reusable methodologies or practical tools that support provenance for curated databases, forcing each project to start from scratch. Research on provenance for scientific databases is still at an early stage, and prototypes have so far proven challenging to deploy or evaluate in the field. Also, most techniques to date focus on provenance within a single database, but this is only part of the problem: real solutions will have to integrate database provenance with the multiple tiers of web applications, and no-one has begun to address this challenge.
The Skye project showed how to build support for curation into the programming language itself, building on recent research on the Links Web programming language, including advances in language-integrated query, and on provenance and data curation. Links is a strongly-typed language that provides state-of-the-art support for language-integrated query and Web programming. This project builds on Links and other recent language designs for heterogeneous meta-programming to develop a new language, called Skye, that can express modular, reusable curation and provenance techniques. To keep focus on the real needs of scientific databases, Skye will be evaluated in the context of GtoPdb and other scientific database projects. Bridging the gap between curation research and the practices of scientific database curators will catalyse a virtuous cycle that will increase the pace of breakthrough results from data-driven science.
Skye draws on the best ideas developed in cutting-edge research on language-integrated query, Web programming, and heterogeneous meta-programming. Skye will provide dialects, or first-class client language definitions, along with translations that map programs written in one dialect to another, or (as a special case) that perform source-to-source translation on a single dialect, for optimisation or to add functionality such as provenance-tracking. These translations will be available as libraries that can change the behaviour of already-written applications by rewriting code, so scientific database developers using Skye will be able to reuse these features instead of having to reimplement them from scratch or make wholesale changes to existing applications.
