Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

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.

The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web

“…However, because efforts to develop and standardize full-featured ontologies for biodiversity science and its related disciplines are well under way [25], we chose to develop a limited “ontology” for the Triplifier that defines only four high-level relationships between class instances. This allowed us to move forward with software development while we wait for richer and more descriptive ontologies to become available.…”

Monitoring Changes in Genetic Diversity

“…Furthermore, other scientific communities have started work on supporting the efforts of the GOs Network, for example through the creation of the Biological Collections Ontology (BCO), which is to provide the informatics stack for the network (Walls et al 2014).…”

Emerging semantics to link phenotype and environment

“…The Biological Collections Ontology (BCO) (Walls et al, 2014a;Walls et al, 2014b;Deck et al, 2015) offers an alternative way to link data, based on ontology design principles from the Ontology for Biomedical Investigations (OBI;Brinkman et al, 2010), adapted for biodiversity science. A key element of BCO is the difference between a specimen collection process, which has a material entity (i.e., specimen) as output and an observing process, which has data as output.…”