title: 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.
authors.affiliation: The iPlant Collaborative, University of Arizona, Tucson, Arizona, United States of America.
authors.forename: Ramona L
authors.initials: RL
authors.lastname: Walls
authors.affiliation: University of California, Berkeley, Berkeley, California, United States of America.
authors.forename: John
authors.initials: J
authors.lastname: Deck
authors.affiliation: Department of Ecology and Evolutionary Biology and the CU Museum of Natural History, University of Colorado at Boulder, Boulder, Colorado, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Guralnick
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.
authors.forename: Steve
authors.initials: S
authors.lastname: Baskauf
authors.affiliation: University of Florida, Florida Museum of Natural History, Gainesville, Florida, United States of America.
authors.forename: Reed
authors.initials: R
authors.lastname: Beaman
authors.affiliation: Research Informatics, California Academy of Sciences, San Francisco, California, United States of America.
authors.forename: Stanley
authors.initials: S
authors.lastname: Blum
authors.affiliation: Gonzaga University, Computer Science, Spokane, Washington, United States of America.
authors.forename: Shawn
authors.initials: S
authors.lastname: Bowers
authors.affiliation: Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Buttigieg
authors.affiliation: University of California, Berkeley, Gump South Pacific Research Station, Moorea, French Polynesia.
authors.forename: Neil
authors.initials: N
authors.lastname: Davies
authors.affiliation: GBIF Norway, Natural History Museum, University in Oslo, Oslo, Norway.
authors.forename: Dag
authors.initials: D
authors.lastname: Endresen
authors.affiliation: LH Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York, United States of America.
authors.forename: Maria Alejandra
authors.initials: MA
authors.lastname: Gandolfo
authors.affiliation: Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada.
authors.forename: Robert
authors.initials: R
authors.lastname: Hanner
authors.affiliation: School of Information Resources and Library Science, University of Arizona, Tucson, Arizona, United States of America.
authors.forename: Alyssa
authors.initials: A
authors.lastname: Janning
authors.affiliation: Biodiversity Institute and Ecology & Evolutionary Biology, The University of Kansas, Lawrence, Kansas, United States of America.
authors.forename: Leonard
authors.initials: L
authors.lastname: Krishtalka
authors.affiliation: University of Florida, Gainesville, Florida, United States of America.
authors.forename: Andréa
authors.initials: A
authors.lastname: Matsunaga
authors.affiliation: Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America.
authors.forename: Peter
authors.initials: P
authors.lastname: Midford
authors.affiliation: The BioVeL Project, School of Computer Science, The University of Manchester, Manchester, United Kingdom.
authors.forename: Norman
authors.initials: N
authors.lastname: Morrison
authors.affiliation: GBIF Secretariat, Copenhagen, Denmark.
authors.forename: Éamonn
authors.initials: É
authors.lastname: Ó Tuama
authors.affiliation: National Center for Ecological Analysis and Synthesis, Santa Barbara, California, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Schildhauer
authors.affiliation: Department of Philosophy, University at Buffalo, Buffalo, New York, United States of America.
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Stucky
authors.affiliation: Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, United States of America.
authors.forename: Andrea
authors.initials: A
authors.lastname: Thomer
authors.affiliation: 3101 VLSB, Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America.
authors.forename: John
authors.initials: J
authors.lastname: Wieczorek
authors.affiliation: Informatics Branch, Information Technology Office, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America.
authors.forename: Jamie
authors.initials: J
authors.lastname: Whitacre
authors.affiliation: University of California San Diego, La Jolla, California, United States of America.
authors.forename: John
authors.initials: J
authors.lastname: Wooley
mesh_terms: D044822:Biodiversity; D019359:Knowledge; D012660:Semantics