Next-generation phenomics for the Tree of Life

J. Gordon Burleigh, Kenzley Alphonse, Andrew J. Alverson, Holly M. Bik, Carrine Blank, Andrea L. Cirranello, Hong Cui, Marymegan Daly, Thomas G. Dietterich, Gail Gasparich, Jed Irvine, Matthew Julius, Seth Kaufman, Edith Law, Jing Liu, Lisa Moore, Maureen A. O'Leary, Maria Passarotti, Sonali Ranade, Nancy B. SimmonsDennis W. Stevenson, Robert W. Thacker, Edward C. Theriot, Sinisa Todorovic, Paúl M. Velazco, Ramona L. Walls, Joanna M. Wolfe, Mengjie Yu

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

The phenotype represents a critical interface between the genome and the environment in which organisms live and evolve. Phenotypic characters also are a rich source of biodiversity data for tree building, and they enable scientists to reconstruct the evolutionary history of organisms, including most fossil taxa, for which genetic data are unavailable. Therefore, phenotypic data are necessary for building a comprehensive Tree of Life. In contrast to recent advances in molecular sequencing, which has become faster and cheaper through recent technological advances, phenotypic data collection remains often prohibitively slow and expensive. The next-generation phenomics project is a collaborative, multidisciplinary effort to leverage advances in image analysis, crowdsourcing, and natural language processing to develop and implement novel approaches for discovering and scoring the phenome, the collection of phentotypic characters for a species. This research represents a new approach to data collection that has the potential to transform phylogenetics research and to enable rapid advances in constructing the Tree of Life. Our goal is to assemble large phenomic datasets built using new methods and to provide the public and scientific community with tools for phenomic data assembly that will enable rapid and automated study of phenotypes across the Tree of Life.

Original languageEnglish (US)
Article numberecurrents.tol.085c713acafc8711b2ff7010a4b03733
JournalPLoS Currents
Issue numberJUNE
DOIs
StatePublished - 2013

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Crowdsourcing
Natural Language Processing
Phenotype
Information Storage and Retrieval
Biodiversity
Research
History
Genome
Datasets

ASJC Scopus subject areas

  • Medicine (miscellaneous)

Cite this

Burleigh, J. G., Alphonse, K., Alverson, A. J., Bik, H. M., Blank, C., Cirranello, A. L., ... Yu, M. (2013). Next-generation phenomics for the Tree of Life. PLoS Currents, (JUNE), [ecurrents.tol.085c713acafc8711b2ff7010a4b03733]. https://doi.org/10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733

Next-generation phenomics for the Tree of Life. / Burleigh, J. Gordon; Alphonse, Kenzley; Alverson, Andrew J.; Bik, Holly M.; Blank, Carrine; Cirranello, Andrea L.; Cui, Hong; Daly, Marymegan; Dietterich, Thomas G.; Gasparich, Gail; Irvine, Jed; Julius, Matthew; Kaufman, Seth; Law, Edith; Liu, Jing; Moore, Lisa; O'Leary, Maureen A.; Passarotti, Maria; Ranade, Sonali; Simmons, Nancy B.; Stevenson, Dennis W.; Thacker, Robert W.; Theriot, Edward C.; Todorovic, Sinisa; Velazco, Paúl M.; Walls, Ramona L.; Wolfe, Joanna M.; Yu, Mengjie.

In: PLoS Currents, No. JUNE, ecurrents.tol.085c713acafc8711b2ff7010a4b03733, 2013.

Research output: Contribution to journalArticle

Burleigh, JG, Alphonse, K, Alverson, AJ, Bik, HM, Blank, C, Cirranello, AL, Cui, H, Daly, M, Dietterich, TG, Gasparich, G, Irvine, J, Julius, M, Kaufman, S, Law, E, Liu, J, Moore, L, O'Leary, MA, Passarotti, M, Ranade, S, Simmons, NB, Stevenson, DW, Thacker, RW, Theriot, EC, Todorovic, S, Velazco, PM, Walls, RL, Wolfe, JM & Yu, M 2013, 'Next-generation phenomics for the Tree of Life', PLoS Currents, no. JUNE, ecurrents.tol.085c713acafc8711b2ff7010a4b03733. https://doi.org/10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733
Burleigh JG, Alphonse K, Alverson AJ, Bik HM, Blank C, Cirranello AL et al. Next-generation phenomics for the Tree of Life. PLoS Currents. 2013;(JUNE). ecurrents.tol.085c713acafc8711b2ff7010a4b03733. https://doi.org/10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733
Burleigh, J. Gordon ; Alphonse, Kenzley ; Alverson, Andrew J. ; Bik, Holly M. ; Blank, Carrine ; Cirranello, Andrea L. ; Cui, Hong ; Daly, Marymegan ; Dietterich, Thomas G. ; Gasparich, Gail ; Irvine, Jed ; Julius, Matthew ; Kaufman, Seth ; Law, Edith ; Liu, Jing ; Moore, Lisa ; O'Leary, Maureen A. ; Passarotti, Maria ; Ranade, Sonali ; Simmons, Nancy B. ; Stevenson, Dennis W. ; Thacker, Robert W. ; Theriot, Edward C. ; Todorovic, Sinisa ; Velazco, Paúl M. ; Walls, Ramona L. ; Wolfe, Joanna M. ; Yu, Mengjie. / Next-generation phenomics for the Tree of Life. In: PLoS Currents. 2013 ; No. JUNE.
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