Database design for ecologists: Composing core entities with observations

Article history: Received 1 January 2007 Received in revised form 11 June 2007 Accepted 30 July 2007 The ecoinformatics community recognizes that ecological synthesis across studies, space, and time will require new informatics tools and infrastructure. Recent advances have been encouraging, butmany problems still face ecologists whomanage their own datasets, prepare data for archiving, and searchdata stores for synthetic research. In this paper,wedescribehow work by the Canopy Database Project (CDP) might enable use of database technology by field ecologists: increasing the quality of database design, improving data validation, and providing structural and semantic metadata — all of which might improve the quality of data archives and thereby help drive ecological synthesis. The CDP has experimented with conceptual components for database design, templates, to address information technology issues facingecologists. Templates represent forest structures and observational measurements on these structures. Using our software, researchers select templates to represent their study’s data and can generate normalized relational databases. Information hidden in those databases is used by ancillary tools, including data intake forms and simple data validation, data visualization, andmetadata export. The primary questionwe address in this paper is, which templates are the right templates. We argue for defining simple templates (with relatively few attributes) that describe the domain's major entities, and for coupling those with focused and flexible observation templates. We present a conceptual model for the observation data type, and show how we have implemented themodel as an observation entity in the DataBank database designer and generator. We show how our visualization tool CanopyView exploits metadata made explicit by DataBank to help scientists with analysis and synthesis. We conclude by presenting future plans for tools to conduct statistical calculations common to forest ecology and to enhance data mining with DataBank databases. DataBank could be extended to another domain by replacing our forest–ecology-specific templates with those for the new domain. This work extends the basic computer science idea of abstract data types and user-defined types to ecology-specific database design tools for individual users, and applies to ecoinformatics the software engineering innovations of domain-specific languages, software patterns, components, refactoring, and end-user programming. © 2007 Elsevier B.V. All rights reserved.