Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

Abstract

The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them. Despite a rapid acceleration in uptake of syntactic and semantic standards for interoperability, it is still difficult for users to find which databases support the standards and interfaces that they need. To solve these problems, several groups are developing registries of databases that capture key metadata describing the biological scope, utility, accessibility, ease-of-use and existence of web services allowing interoperability between resources. Here, we describe some of these initiatives including a novel formalism, the Database Description Framework, for describing database operations and functionality and encouraging good database practise. We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf.

Figure 1.

The DDF query and annotation tool. This tool allows any user to browse a set of resources that have been annotated using the DDF categories. Searches for resources by DDF category and level are also possible. In addition, resource maintainers can log-in and edit their existing annotations or annotate a new resource using a simple web form. This tool is freely available and easy to install for other communities that wish to create their own registry of resources.