02428nas a2200397   4500000000100000000000100001008004100002260000900043100001700052700001800069700001900087700001800106700001800124700001700142700001500159700001900174700002600193700001800219700002400237700002100261700001900282700001400301700001500315700001700330700001800347700001900365700001700384700001400401700001800415700001600433245005800449300001000507490000600517520149300523022001402016       2015                            d  c20151 aAnne Thessen1 aDaniel Bunker1 aPier Buttigieg1 aLaurel Cooper1 aWasila Dahdul1 aSami Domisch1 aNico Franz1 aPankaj Jaiswal1 aCarolyn Lawrence-Dill1 aPeter Midford1 aChristopher Mungall1 aMartín Ramírez1 aChelsea Specht1 aLars Vogt1 aRutger Vos1 aRamona Walls1 aJeffrey White1 aGuanyang Zhang1 aAndrew Deans1 aEva Huala1 aSuzanna Lewis1 aPaula Mabee00aEmerging semantics to link phenotype and environment.  ae14700 v33 aUnderstanding 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.  a2167-8359