Emerging semantics to link phenotype and environment

• Autores: Thessen, Anne E.; Bunker, Daniel E.; Buttigieg, Pier Luigi; Cooper, Laurel D.; Dahdul, Wasila M.; Domisch, Sami; Franz, Nico M.; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J.; Midford, Peter E.; Mungall, Christopher J.; Ramirez, Martin Javier; Specht, Chelsea D.; Vogt, Lars; Vos, Rutger Aldo; Walls, Ramona L.; White, Jeffrey W.; Zhang, Guanyang; Deans, Andrew R.; Huala, Eva; Lewis, Suzanna E.; Mabee, Paula M.
• Año de publicación: 2015
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: Phenotype; Environment; Ontology; Semantic web; Biodiversity; Data integration
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

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.
Fil: Thessen, Anne E.. Ronin Institute for Independent Scholarship; Estados Unidos
Fil: Bunker, Daniel E.. New Jersey Institute of Technology; Estados Unidos
Fil: Buttigieg, Pier Luigi. Helmholtz-Zentrum für Polar-und Meeresforschung; Alemania
Fil: Cooper, Laurel D.. State University of Oregon; Estados Unidos
Fil: Dahdul, Wasila M.. University of South Dakota; Estados Unidos
Fil: Domisch, Sami. University of Yale; Estados Unidos
Fil: Franz, Nico M.. Arizona State University; Estados Unidos
Fil: Jaiswal, Pankaj. State University of Oregon; Estados Unidos
Fil: Lawrence-Dill, Carolyn J.. University of Iowa; Estados Unidos
Fil: Midford, Peter E.. No especifica;
Fil: Mungall, Christopher J.. Lawrence Berkeley National Laboratory; Estados Unidos
Fil: Ramirez, Martin Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Fil: Specht, Chelsea D.. University of California at Berkeley; Estados Unidos
Fil: Vogt, Lars. Universitat Bonn; Alemania
Fil: Vos, Rutger Aldo. Naturalis Biodiversity Center; Países Bajos
Fil: Walls, Ramona L.. Arizona State University; Estados Unidos
Fil: White, Jeffrey W.. United States Department of Agriculture; Estados Unidos
Fil: Zhang, Guanyang. Arizona State University; Estados Unidos
Fil: Deans, Andrew R.. State University of Pennsylvania; Estados Unidos
Fil: Huala, Eva. Phoenix Bioinformatics; Estados Unidos
Fil: Lewis, Suzanna E.. Lawrence Berkeley National Laboratory; Estados Unidos
Fil: Mabee, Paula M.. University of South Dakota; Estados Unidos