Abstract
The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.
Highlights
The loss of biodiversity is a major societal issue of our time, impacting the need for food, fuel, fiber, and animal feed [1,2,3]
The most current stable version of the Biological Collections Ontology (BCO) is always available at http://purl.obolibrary. org/obo/bco.owl and can be browsed via BioPortal at http:// bioportal.bioontology.org/ontologies/BCO
The development of ontologies for biodiversity sciences aims to overcome several shortcomings of the current state of affairs: 1) a lack of clarity in the definitions of terms currently used for biodiversity data, 2) the inability to reason over complex data sets due to a lack of well-structured logical definitions, and 3) an inability to integrate museum collection data with other large biological data sets such as the Gene Ontology (GO) database, environmental or metagenomic data, and survey-based data
Summary
The loss of biodiversity is a major societal issue of our time, impacting the need for food, fuel, fiber, and animal feed [1,2,3]. Recognition of the accelerating loss of biodiversity has prompted immediate, global action, including initiatives such as the Convention on Biological Diversity (CBD) – an agreement between 150 countries dedicated to sustainable development [4] – and the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). These initiatives require scientific research into underlying biological, physical, and chemical processes to develop predictive models and inform policy decisions. Biodiversity data are highly heterogeneous, including information about organisms, their morphology and genetics, life history and habitats, and geographical ranges. The means to properly describe and interrelate these different data sources and types is essential if such resources are to fulfill their potential for flexible use and re-use in a wide variety of monitoring, scientific, and policy-oriented applications [5]
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