An ontology for describing and synthesizing ecological observation data

Abstract

Research in ecology increasingly relies on the integration of small, focused studies, to produce larger datasets that allow for more powerful, synthetic analyses. The results of these synthetic analyses are critical in guiding decisions about how to sustainably manage our natural environment, so it is important for researchers to effectively discover relevant data, and appropriately integrate these within their analyses. However, ecological data encompasses an extremely broad range of data types, structures, and semantic concepts. Moreover, ecological data is widely distributed, with few well-established repositories or standard protocols for their archiving and retrieval. These factors make the discovery and integration of ecological data sets a highly labor-intensive task. Metadata standards such as the Ecological Metadata Language and Darwin Core are important steps for improving our ability to discover and access ecological data, but are limited to describing only a few, relatively specific aspects of data content ( e.g., data owner and contact information, variable “names”, keyword descriptions, etc.). A more flexible and powerful way to capture the semantic subtleties of complex ecological data, its structure and contents, and the inter-relationships among data variables is needed. We present a formal ontology for capturing the semantics of generic scientific observation and measurement. The ontology provides a convenient basis for adding detailed semantic annotations to scientific data, which crystallize the inherent “meaning” of observational data. The ontology can be used to characterize the context of an observation ( e.g., space and time), and clarify inter-observational relationships such as dependency hierarchies ( e.g., nested experimental observations) and meaningful dimensions within the data ( e.g., axes for cross-classified categorical summarization). It also enables the robust description of measurement units ( e.g., grams of carbon per liter of seawater), and can facilitate automatic unit conversions ( e.g., pounds to kilograms). The ontology can be easily extended with specialized domain vocabularies, making it both broadly applicable and highly customizable. Finally, we describe the utility of the ontology for enriching the capabilities of data discovery and integration processes.