Finding our way through phenotypes

A. R. Deans; S. E. Lewis; E. Huala; S. S. Anzaldo; M. Ashburner; J. P. Balhoff; D. C. Blackburn; J. A. Blake; J. G. Burleigh; B. Chanet; L. D. Cooper; M. Courtot; S. Csosz; H. Cui; W. Dahdul; S. Das; T. A. Dececchi; A. Dettai; R. Diogo; R. E. Druzinsky; M. Dumontier; N. M. Franz; F. Friedrich; G. V. Gkoutos; M. Haendel; L. J. Harmon; T. F. Hayamizu; Y. He; H. M. Hines; N. Ibrahim; L. M. Jackson; P. Jaiswal; C. James-Zorn; S. Kohler; G. Lecointre; H. Lapp; C. J. Lawrence; N. Le Novere; J. G. Lundberg; J. Macklin; A. R. Mast; P. E. Midford; I. Miko; C. J. Mungall; A. Oellrich; D. Osumi-Sutherland; H. Parkinson; M. J. Ramirez; S. Richter; P. N. Robinson; A. Ruttenberg; K. S. Schulz; E. Segerdell; K. C. Seltmann; M. J. Sharkey; A. D. Smith; B. Smith; C. D. Specht; R. B. Squires; R. W. Thacker; A. Thessen; J. Fernandez-Triana; M. Vihinen; P. D. Vize; L. Vogt; C. E. Wall; R. L. Walls; M. Westerfeld; R. A. Wharton; C. S. Wirkner; J. B. Woolley; M. J. Yoder; A. M. Zorn; P. Mabee

doi:10.1371/journal.pbio.1002033

Finding our way through phenotypes

A. R. Deans, S. E. Lewis, E. Huala, S. S. Anzaldo, M. Ashburner, J. P. Balhoff, D. C. Blackburn, J. A. Blake, J. G. Burleigh, B. Chanet, L. D. Cooper, M. Courtot, S. Csosz, H. Cui, W. Dahdul, S. Das, T. A. Dececchi, A. Dettai, R. Diogo, R. E. DruzinskyM. Dumontier, N. M. Franz, F. Friedrich, G. V. Gkoutos, M. Haendel, L. J. Harmon, T. F. Hayamizu, Y. He, H. M. Hines, N. Ibrahim, L. M. Jackson, P. Jaiswal, C. James-Zorn, S. Kohler, G. Lecointre, H. Lapp, C. J. Lawrence, N. Le Novere, J. G. Lundberg, J. Macklin, A. R. Mast, P. E. Midford, I. Miko, C. J. Mungall, A. Oellrich, D. Osumi-Sutherland, H. Parkinson, M. J. Ramirez, S. Richter, P. N. Robinson, A. Ruttenberg, K. S. Schulz, E. Segerdell, K. C. Seltmann, M. J. Sharkey, A. D. Smith, B. Smith, C. D. Specht, R. B. Squires, R. W. Thacker, A. Thessen, J. Fernandez-Triana, M. Vihinen, P. D. Vize, L. Vogt, C. E. Wall, R. L. Walls, M. Westerfeld, R. A. Wharton, C. S. Wirkner, J. B. Woolley, M. J. Yoder, A. M. Zorn, P. Mabee

Cancer and Genomic Sciences

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128 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 language	English
Pages (from-to)	e1002033
Journal	PLoS Biol.
Volume	13
Issue number	1
DOIs	https://doi.org/10.1371/journal.pbio.1002033
Publication status	Published - 6 Jan 2015

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Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., Burleigh, J. G., Chanet, B., Cooper, L. D., Courtot, M., Csosz, S., Cui, H., Dahdul, W., Das, S., Dececchi, T. A., Dettai, A., Diogo, R., ... Mabee, P. (2015). Finding our way through phenotypes. PLoS Biol., 13(1), e1002033. https://doi.org/10.1371/journal.pbio.1002033

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title = "Finding our way through phenotypes",

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.",

author = "Deans, {A. R.} and Lewis, {S. E.} and E. Huala and Anzaldo, {S. S.} and M. Ashburner and Balhoff, {J. P.} and Blackburn, {D. C.} and Blake, {J. A.} and Burleigh, {J. G.} and B. Chanet and Cooper, {L. D.} and M. Courtot and S. Csosz and H. Cui and W. Dahdul and S. Das and Dececchi, {T. A.} and A. Dettai and R. Diogo and Druzinsky, {R. E.} and M. Dumontier and Franz, {N. M.} and F. Friedrich and Gkoutos, {G. V.} and M. Haendel and Harmon, {L. J.} and Hayamizu, {T. F.} and Y. He and Hines, {H. M.} and N. Ibrahim and Jackson, {L. M.} and P. Jaiswal and C. James-Zorn and S. Kohler and G. Lecointre and H. Lapp and Lawrence, {C. J.} and {Le Novere}, N. and Lundberg, {J. G.} and J. Macklin and Mast, {A. R.} and Midford, {P. E.} and I. Miko and Mungall, {C. J.} and A. Oellrich and D. Osumi-Sutherland and H. Parkinson and Ramirez, {M. J.} and S. Richter and Robinson, {P. N.} and A. Ruttenberg and Schulz, {K. S.} and E. Segerdell and Seltmann, {K. C.} and Sharkey, {M. J.} and Smith, {A. D.} and B. Smith and Specht, {C. D.} and Squires, {R. B.} and Thacker, {R. W.} and A. Thessen and J. Fernandez-Triana and M. Vihinen and Vize, {P. D.} and L. Vogt and Wall, {C. E.} and Walls, {R. L.} and M. Westerfeld and Wharton, {R. A.} and Wirkner, {C. S.} and Woolley, {J. B.} and Yoder, {M. J.} and Zorn, {A. M.} and P. Mabee",

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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, Csosz, 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, Kohler, S, Lecointre, G, Lapp, H, Lawrence, CJ, Le Novere, N, Lundberg, JG, Macklin, J, Mast, AR, Midford, PE, Miko, I, Mungall, CJ, Oellrich, A, Osumi-Sutherland, D, Parkinson, H, Ramirez, 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 Biol., vol. 13, no. 1, pp. e1002033. https://doi.org/10.1371/journal.pbio.1002033

TY - JOUR

T1 - Finding our way through phenotypes

AU - Deans, A. R.

AU - Lewis, S. E.

AU - Huala, E.

AU - Anzaldo, S. S.

AU - Ashburner, M.

AU - Balhoff, J. P.

AU - Blackburn, D. C.

AU - Blake, J. A.

AU - Burleigh, J. G.

AU - Chanet, B.

AU - Cooper, L. D.

AU - Courtot, M.

AU - Csosz, S.

AU - Cui, H.

AU - Dahdul, W.

AU - Das, S.

AU - Dececchi, T. A.

AU - Dettai, A.

AU - Diogo, R.

AU - Druzinsky, R. E.

AU - Dumontier, M.

AU - Franz, N. M.

AU - Friedrich, F.

AU - Gkoutos, G. V.

AU - Haendel, M.

AU - Harmon, L. J.

AU - Hayamizu, T. F.

AU - He, Y.

AU - Hines, H. M.

AU - Ibrahim, N.

AU - Jackson, L. M.

AU - Jaiswal, P.

AU - James-Zorn, C.

AU - Kohler, S.

AU - Lecointre, G.

AU - Lapp, H.

AU - Lawrence, C. J.

AU - Le Novere, N.

AU - Lundberg, J. G.

AU - Macklin, J.

AU - Mast, A. R.

AU - Midford, P. E.

AU - Miko, I.

AU - Mungall, C. J.

AU - Oellrich, A.

AU - Osumi-Sutherland, D.

AU - Parkinson, H.

AU - Ramirez, M. J.

AU - Richter, S.

AU - Robinson, P. N.

AU - Ruttenberg, A.

AU - Schulz, K. S.

AU - Segerdell, E.

AU - Seltmann, K. C.

AU - Sharkey, M. J.

AU - Smith, A. D.

AU - Smith, B.

AU - Specht, C. D.

AU - Squires, R. B.

AU - Thacker, R. W.

AU - Thessen, A.

AU - Fernandez-Triana, J.

AU - Vihinen, M.

AU - Vize, P. D.

AU - Vogt, L.

AU - Wall, C. E.

AU - Walls, R. L.

AU - Westerfeld, M.

AU - Wharton, R. A.

AU - Wirkner, C. S.

AU - Woolley, J. B.

AU - Yoder, M. J.

AU - Zorn, A. M.

AU - Mabee, P.

PY - 2015/1/6

Y1 - 2015/1/6

N2 - 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.

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.

U2 - 10.1371/journal.pbio.1002033

DO - 10.1371/journal.pbio.1002033

M3 - Article

SN - 1545-7885

VL - 13

SP - e1002033

JO - PLoS Biol.

JF - PLoS Biol.

IS - 1

ER -

Finding our way through phenotypes

Abstract

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