Cross-tier Web Programming for Curated Databases: a Case Study

Abstract

Curated databases have become important sources of information across several scientific disciplines, and as the result of 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 the 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 relational database itself, but also an ecosystem of web applications to display the data, and applications which allow 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 can 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 towards this goal, 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 front end of a real world scientific database, the IUPHAR/BPS Guide to Pharmacology (GtoPdb), in the Links cross-tier programming language. We show how programming language features such as language-integrated query simplify the development process, and rule out common errors. Through a comparative performance evaluation, we show that the Links implementation performs fewer database queries, while the time needed to handle the queries is comparable to the Java version. Furthermore, while there is some overhead to using Links because of its comparative immaturity compared to Java, the Links version is usable as a proof-of-concept case study of cross-tier programming for curated databases.

[ This paper is a conference pre-print presented at IDCC 2020 after lightweight peer review. The most up-to-date version of the paper can be found on arXiv https://arxiv.org/abs/2003.03845 ]