Finding Our Way through Phenotypes

Andrew Robert Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Wasila Dahdul, Sandip Das, T. Alexander Dececchi, Agnes Dettai, Rui Diogo, Robert E. Druzinsky & 54 others Michel Dumontier, Nico M. Franz, Frank Friedrich, George V. Gkoutos, Melissa Haendel, Luke J. Harmon, Terry F. Hayamizu, Yongqun He, Heather M. Hines, Nizar Ibrahim, Laura M. Jackson, Pankaj Jaiswal, Christina James-Zorn, Sebastian Köhler, Guillaume Lecointre, Hilmar Lapp, Carolyn J. Lawrence, Nicolas Le Novère, John G. Lundberg, James Macklin, Austin R. Mast, Peter E. Midford, Istvan Miko, Christopher J. Mungall, Anika Oellrich, David Osumi-Sutherland, Helen Parkinson, Martín J. Ramírez, Stefan Richter, Peter N. Robinson, Alan Ruttenberg, Katja S. Schulz, Erik Segerdell, Katja C. Seltmann, Michael J. Sharkey, Aaron D. Smith, Barry Smith, Chelsea D. Specht, R. Burke Squires, Robert W. Thacker, Anne Thessen, Jose Fernandez-Triana, Mauno Vihinen, Peter D. Vize, Lars Vogt, Christine E. Wall, Ramona L. Walls, Monte Westerfeld, Robert A. Wharton, Christian S. Wirkner, James B. Woolley, Matthew J. Yoder, Aaron M. Zorn, Paula Mabee

Research output: Contribution to journalArticle

100 Citations (Scopus)

Abstract

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

Original languageEnglish (US)
JournalPLoS biology
Volume13
Issue number1
DOIs
StatePublished - Jan 1 2015

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Data description
Phenotype
phenotype
Biological Sciences
Ecology
Medicine
genomics
Metagenomics
Systems Biology
pressing
Genomics
funding
reproducibility
data analysis
Consensus
medicine
Language
taxonomy
ecology
phenomics

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., ... Mabee, P. (2015). Finding Our Way through Phenotypes. PLoS biology, 13(1). https://doi.org/10.1371/journal.pbio.1002033
Deans, Andrew Robert ; Lewis, Suzanna E. ; Huala, Eva ; Anzaldo, Salvatore S. ; Ashburner, Michael ; Balhoff, James P. ; Blackburn, David C. ; Blake, Judith A. ; Burleigh, J. Gordon ; Chanet, Bruno ; Cooper, Laurel D. ; Courtot, Mélanie ; Csösz, Sándor ; Cui, Hong ; Dahdul, Wasila ; Das, Sandip ; Dececchi, T. Alexander ; Dettai, Agnes ; Diogo, Rui ; Druzinsky, Robert E. ; Dumontier, Michel ; Franz, Nico M. ; Friedrich, Frank ; Gkoutos, George V. ; Haendel, Melissa ; Harmon, Luke J. ; Hayamizu, Terry F. ; He, Yongqun ; Hines, Heather M. ; Ibrahim, Nizar ; Jackson, Laura M. ; Jaiswal, Pankaj ; James-Zorn, Christina ; Köhler, Sebastian ; Lecointre, Guillaume ; Lapp, Hilmar ; Lawrence, Carolyn J. ; Le Novère, Nicolas ; Lundberg, John G. ; Macklin, James ; Mast, Austin R. ; Midford, Peter E. ; Miko, Istvan ; Mungall, Christopher J. ; Oellrich, Anika ; Osumi-Sutherland, David ; Parkinson, Helen ; Ramírez, Martín J. ; Richter, Stefan ; Robinson, Peter N. ; Ruttenberg, Alan ; Schulz, Katja S. ; Segerdell, Erik ; Seltmann, Katja C. ; Sharkey, Michael J. ; Smith, Aaron D. ; Smith, Barry ; Specht, Chelsea D. ; Squires, R. Burke ; Thacker, Robert W. ; Thessen, Anne ; Fernandez-Triana, Jose ; Vihinen, Mauno ; Vize, Peter D. ; Vogt, Lars ; Wall, Christine E. ; Walls, Ramona L. ; Westerfeld, Monte ; Wharton, Robert A. ; Wirkner, Christian S. ; Woolley, James B. ; Yoder, Matthew J. ; Zorn, Aaron M. ; Mabee, Paula. / Finding Our Way through Phenotypes. In: PLoS biology. 2015 ; Vol. 13, No. 1.
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abstract = "Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.",
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Deans, AR, Lewis, SE, Huala, E, Anzaldo, SS, Ashburner, M, Balhoff, JP, Blackburn, DC, Blake, JA, Burleigh, JG, Chanet, B, Cooper, LD, Courtot, M, Csösz, S, Cui, H, Dahdul, W, Das, S, Dececchi, TA, Dettai, A, Diogo, R, Druzinsky, RE, Dumontier, M, Franz, NM, Friedrich, F, Gkoutos, GV, Haendel, M, Harmon, LJ, Hayamizu, TF, He, Y, Hines, HM, Ibrahim, N, Jackson, LM, Jaiswal, P, James-Zorn, C, Köhler, S, Lecointre, G, Lapp, H, Lawrence, CJ, Le Novère, N, Lundberg, JG, Macklin, J, Mast, AR, Midford, PE, Miko, I, Mungall, CJ, Oellrich, A, Osumi-Sutherland, D, Parkinson, H, Ramírez, MJ, Richter, S, Robinson, PN, Ruttenberg, A, Schulz, KS, Segerdell, E, Seltmann, KC, Sharkey, MJ, Smith, AD, Smith, B, Specht, CD, Squires, RB, Thacker, RW, Thessen, A, Fernandez-Triana, J, Vihinen, M, Vize, PD, Vogt, L, Wall, CE, Walls, RL, Westerfeld, M, Wharton, RA, Wirkner, CS, Woolley, JB, Yoder, MJ, Zorn, AM & Mabee, P 2015, 'Finding Our Way through Phenotypes', PLoS biology, vol. 13, no. 1. https://doi.org/10.1371/journal.pbio.1002033

Finding Our Way through Phenotypes. / Deans, Andrew Robert; Lewis, Suzanna E.; Huala, Eva; Anzaldo, Salvatore S.; Ashburner, Michael; Balhoff, James P.; Blackburn, David C.; Blake, Judith A.; Burleigh, J. Gordon; Chanet, Bruno; Cooper, Laurel D.; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T. Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E.; Dumontier, Michel; Franz, Nico M.; Friedrich, Frank; Gkoutos, George V.; Haendel, Melissa; Harmon, Luke J.; Hayamizu, Terry F.; He, Yongqun; Hines, Heather M.; Ibrahim, Nizar; Jackson, Laura M.; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J.; Le Novère, Nicolas; Lundberg, John G.; Macklin, James; Mast, Austin R.; Midford, Peter E.; Miko, Istvan; Mungall, Christopher J.; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J.; Richter, Stefan; Robinson, Peter N.; Ruttenberg, Alan; Schulz, Katja S.; Segerdell, Erik; Seltmann, Katja C.; Sharkey, Michael J.; Smith, Aaron D.; Smith, Barry; Specht, Chelsea D.; Squires, R. Burke; Thacker, Robert W.; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D.; Vogt, Lars; Wall, Christine E.; Walls, Ramona L.; Westerfeld, Monte; Wharton, Robert A.; Wirkner, Christian S.; Woolley, James B.; Yoder, Matthew J.; Zorn, Aaron M.; Mabee, Paula.

In: PLoS biology, Vol. 13, No. 1, 01.01.2015.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Finding Our Way through Phenotypes

AU - Deans, Andrew Robert

AU - Lewis, Suzanna E.

AU - Huala, Eva

AU - Anzaldo, Salvatore S.

AU - Ashburner, Michael

AU - Balhoff, James P.

AU - Blackburn, David C.

AU - Blake, Judith A.

AU - Burleigh, J. Gordon

AU - Chanet, Bruno

AU - Cooper, Laurel D.

AU - Courtot, Mélanie

AU - Csösz, Sándor

AU - Cui, Hong

AU - Dahdul, Wasila

AU - Das, Sandip

AU - Dececchi, T. Alexander

AU - Dettai, Agnes

AU - Diogo, Rui

AU - Druzinsky, Robert E.

AU - Dumontier, Michel

AU - Franz, Nico M.

AU - Friedrich, Frank

AU - Gkoutos, George V.

AU - Haendel, Melissa

AU - Harmon, Luke J.

AU - Hayamizu, Terry F.

AU - He, Yongqun

AU - Hines, Heather M.

AU - Ibrahim, Nizar

AU - Jackson, Laura M.

AU - Jaiswal, Pankaj

AU - James-Zorn, Christina

AU - Köhler, Sebastian

AU - Lecointre, Guillaume

AU - Lapp, Hilmar

AU - Lawrence, Carolyn J.

AU - Le Novère, Nicolas

AU - Lundberg, John G.

AU - Macklin, James

AU - Mast, Austin R.

AU - Midford, Peter E.

AU - Miko, Istvan

AU - Mungall, Christopher J.

AU - Oellrich, Anika

AU - Osumi-Sutherland, David

AU - Parkinson, Helen

AU - Ramírez, Martín J.

AU - Richter, Stefan

AU - Robinson, Peter N.

AU - Ruttenberg, Alan

AU - Schulz, Katja S.

AU - Segerdell, Erik

AU - Seltmann, Katja C.

AU - Sharkey, Michael J.

AU - Smith, Aaron D.

AU - Smith, Barry

AU - Specht, Chelsea D.

AU - Squires, R. Burke

AU - Thacker, Robert W.

AU - Thessen, Anne

AU - Fernandez-Triana, Jose

AU - Vihinen, Mauno

AU - Vize, Peter D.

AU - Vogt, Lars

AU - Wall, Christine E.

AU - Walls, Ramona L.

AU - Westerfeld, Monte

AU - Wharton, Robert A.

AU - Wirkner, Christian S.

AU - Woolley, James B.

AU - Yoder, Matthew J.

AU - Zorn, Aaron M.

AU - Mabee, Paula

PY - 2015/1/1

Y1 - 2015/1/1

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AB - Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

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Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP et al. Finding Our Way through Phenotypes. PLoS biology. 2015 Jan 1;13(1). https://doi.org/10.1371/journal.pbio.1002033