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

dc.contributor.authorWalls, Ramona L.
dc.contributor.authorDeck, John
dc.contributor.authorGuralnick, Robert
dc.contributor.authorBaskauf, Steve
dc.contributor.authorBeaman, Reed
dc.contributor.authorBlum, Stanley
dc.contributor.authorBowers, Shawn
dc.contributor.authorButtigieg, Pier Luigi
dc.contributor.authorDavies, Neil
dc.contributor.authorEndresen, Dag
dc.contributor.authorGandolfo, Maria Alejandra
dc.contributor.authorHanner, Robert
dc.contributor.authorJanning, Alyssa
dc.contributor.authorKrishtalka, Leonard
dc.contributor.authorMatsunaga, Andréa
dc.contributor.authorMidford, Peter
dc.contributor.authorMorrison, Norman
dc.contributor.authorTuama, Éamonn Ó.
dc.contributor.authorSchildhauer, Mark
dc.contributor.authorSmith, Barry
dc.contributor.authorStucky, Brian J.
dc.contributor.authorThomer, Andrea
dc.contributor.authorWieczorek, John
dc.contributor.authorWhitacre, Jamie
dc.contributor.authorWooley, John
dc.date.accessioned2018-04-02T15:49:47Z
dc.date.available2018-04-02T15:49:47Z
dc.date.issued2014-03-03
dc.identifier.citationWalls RL, Deck J, Guralnick R, Baskauf S, Beaman R, Blum S, et al. (2014) Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. PLoS ONE 9(3): e89606. https://doi.org/10.1371/journal.pone.0089606en_US
dc.identifier.urihttp://hdl.handle.net/1803/8805
dc.description.abstractThe 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.en_US
dc.language.isoen_USen_US
dc.publisherPLOS ONEen_US
dc.subjectknowledge discoveryen_US
dc.subjectsemanticsen_US
dc.subjectontologyen_US
dc.subjectbiodiversityen_US
dc.subjectbiological diversityen_US
dc.titleSemantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologiesen_US
dc.typeArticleen_US


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