TY - JOUR
AU - Anne Thessen
AU - Daniel Bunker
AU - Pier Buttigieg
AU - Laurel Cooper
AU - Wasila Dahdul
AU - Sami Domisch
AU - Nico Franz
AU - Pankaj Jaiswal
AU - Carolyn Lawrence-Dill
AU - Peter Midford
AU - Christopher Mungall
AU - Martín Ramírez
AU - Chelsea Specht
AU - Lars Vogt
AU - Rutger Vos
AU - Ramona Walls
AU - Jeffrey White
AU - Guanyang Zhang
AU - Andrew Deans
AU - Eva Huala
AU - Suzanna Lewis
AU - Paula Mabee
AB - 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.
BT - PeerJ
C1 - http://www.ncbi.nlm.nih.gov/pubmed/26713234?dopt=Abstract
DA - 2015
DO - 10.7717/peerj.1470
J2 - PeerJ
LA - eng
N2 - 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.
PY - 2015
EP - e1470
T2 - PeerJ
TI - Emerging semantics to link phenotype and environment.
VL - 3
SN - 2167-8359
ER -