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Emerging semantics to link phenotype and environment

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  • 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.
  • This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/
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  • Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. 2015. Emerging semantics to link phenotype and environment. PeerJ 3:e1470 https://doi.org/10.7717/peerj.1470
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  • The scientific meeting from which this review arose was organized by the Phenotype Research Coordination Network, which is funded by the US National Science Foundation, grant number DEB-0956049. PLB's work on this project is supported through the Micro B3 project, funded by the European Union's Seventh Framework Programme (Joint Call OCEAN.2011-2: marine microbial diversity-new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589. SD received funding from the German Research Foundation DFG (grant DO 1880/1-1). PJ and LDC received funding from the US National Science Foundation (NSF IOS:0822201, IOS:1127112, IOS:1340112). CDS received funding from the US National Science Foundation grant number DEB 1208666. RLW was supported by the iPlant collaborative as part of the National Science Foundation Award Numbers DBI-0735191 and DBI-1265383. CJM and SEL were supported by R24OD011883 and by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231. PMM and WMD were supported through by Phenoscape project (NSF grants DBI-1062404 and DBI-1062542).
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