Missouri Botanical Garden Open Conference Systems, TDWG 2013 ANNUAL CONFERENCE

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Linking Biodiversity Data with the Biological Collections Ontology
Ramona Walls, John Deck, Robert Guralnick, John Wieczorek

Building: Grand Hotel Mediterraneo
Room: Sala dei Continenti
Date: 2013-11-01 09:20 AM – 09:33 AM
Last modified: 2013-10-07

Abstract


The Biological Collections Ontology (BCO) is a new ontology that aims to improve data aggregation and integration across the biodiversity domain. It can be used to describe physical samples and sampling processes such as specimen collection or DNA isolation, as well as observations that involve no physical sampling. It encompasses 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 potentially many organisms, especially microbes, and 3) survey-based ecological observations. Although terminologies such as Darwin Core (DwC) and Access to Biological Collection Data (ABCD) provide a controlled vocabulary for many aspects of biodiversity, they lack the semantic structure needed to perform complex queries over diverse data sets. The BCO is being developed according to the Open Biological and Biomedical Ontologies (OBO) Foundry principles, which makes it easy to incorporate existing ontology terms and relations drawn from multiple OBO Foundry Ontologies. For example, the BCO includes terms from the Basic Formal Ontology (a domain neutral, upper-level ontology), the Information Artifact Ontology, the Ontology for Biomedical Investigations, and the Common Anatomy Reference Ontology. In addition, BCO terminology can be combined with terms from the Population and Community Ontology and the Environment Ontology to more fully describe biological samples and sampling events. In this presentation, we will present the work to date on the BCO and provide a demonstration of how it can be used to query biodiversity data. In addition, we will address some of the challenges involved in retrofitting legacy data to an ontology and discuss BCO’s relationship to existing standards such as DwC and the MIxS standard for metagenomic data.