title: Emerging semantics to link phenotype and environment.
abstract: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.
authors.affiliation: Ronin Institute for Independent Scholarship , Monclair, NJ , United States ; The Data Detektiv , Waltham, MA , United States.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Thessen
authors.affiliation: Department of Biological Sciences, New Jersey Institute of Technology , Newark, NJ , United States.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Bunker
authors.affiliation: HGF-MPG Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar-und Meeresforschung , Bremerhaven , Germany.
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Buttigieg
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , United States.
authors.forename: Laurel D
authors.initials: LD
authors.lastname: Cooper
authors.affiliation: Department of Biology, University of South Dakota , Vermillion, SD , United States.
authors.forename: Wasila M
authors.initials: WM
authors.lastname: Dahdul
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT , United States.
authors.forename: Sami
authors.initials: S
authors.lastname: Domisch
authors.affiliation: School of Life Sciences, Arizona State University , Tempe, AZ , United States.
authors.forename: Nico M
authors.initials: NM
authors.lastname: Franz
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , United States.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
authors.affiliation: Departments of Genetics, Development and Cell Biology and Agronomy, Iowa State University , Ames, IA , United States.
authors.forename: Carolyn J
authors.initials: CJ
authors.lastname: Lawrence-Dill
authors.affiliation: Richmond, VA , United States.
authors.forename: Peter E
authors.initials: PE
authors.lastname: Midford
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, CA , United States.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
authors.affiliation: Division of Arachnology, Museo Argentino de Ciencias Naturales-CONICET , Buenos Aires , Argentina.
authors.forename: Martín J
authors.initials: MJ
authors.lastname: Ramírez
authors.affiliation: Departments of Plant and Microbial Biology & Integrative Biology, University of California , Berkeley, CA , United States.
authors.forename: Chelsea D
authors.initials: CD
authors.lastname: Specht
authors.affiliation: Institut für Evolutionsbiologie und Ökologie, Universität Bonn , Bonn , Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Vogt
authors.affiliation: Naturalis Biodiversity Center , Leiden , The Netherlands.
authors.forename: Rutger Aldo
authors.initials: RA
authors.lastname: Vos
authors.affiliation: iPlant Collaborative, University of Arizona , Tucson, AZ , United States.
authors.forename: Ramona L
authors.initials: RL
authors.lastname: Walls
authors.affiliation: US Arid Land Agricultural Research Center, United States Department of Agriculture-ARS , Maricopa, AZ , United States.
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: White
authors.affiliation: School of Life Sciences, Arizona State University , Tempe, AZ , United States.
authors.forename: Guanyang
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Department of Entomology, Pennsylvania State University , University Park, PA , United States.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Deans
authors.affiliation: Phoenix Bioinformatics , Redwood City, CA , United States.
authors.forename: Eva
authors.initials: E
authors.lastname: Huala
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, CA , United States.
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
authors.affiliation: Department of Biology, University of South Dakota , Vermillion, SD , United States.
authors.forename: Paula M
authors.initials: PM
authors.lastname: Mabee
keywords: Biodiversity; Data integration; Environment; Ontology; Phenotype; Semantic web