Abstract

Curated databases have become important sources of information across scientific disciplines, and due to the manual work of experts, often become important reference works. Features such as provenance tracking, archiving, and data citation are widely regarded as important features for curated databases, but implementing such features is challenging, and small database projects often lack the resources to do so. A scientific database application is not just the database itself, but also an ecosystem of web applications to display the data, and applications supporting data curation. Supporting advanced curation features requires changing all of these components, and there is currently no way to provide such capabilities in a reusable way. Cross-tier programming languages have been proposed to simplify the creation of web applications, where developers write an application in a single, uniform language. Consequently, database queries and updates can be written in the same language as the rest of the program, and at least in principle, it should be possible to provide curation features reusably via program transformations. As a first step, it is important to establish that realistic curated databases can be implemented in a cross-tier programming language. In this paper, we describe such a case study: reimplementing the web frontend of a real-world scientific database, the IUPHAR/BPS Guide to Pharmacology (GtoPdb), in the Links programming language. We show how features such as language-integrated query simplify the development process, and rule out common errors. We show that the Links implementation performs fewer database queries, while the time needed to handle the queries is comparable to the Java version. While there is some overhead to using Links because of its comparative immaturity compared to Java, the Links version is viable as a proof-of-concept case study.

Citation information

Cross-tier web programming for curated databases: a case study, Simon Fowler, Simon Harding, Joanna Sharman, and James Cheney. IJDC 16(1), 2021.

Turing affiliated authors