Finding Our Way through Phenotypes

Andrew R. 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; Melanie Courtot; Sandor Csoesz; Hong Cui; Wasila Dahdul; Sandip Das; T. Alexander Dececchi; Agnes Dettai; Rui Diogo; Robert E. Druzinsky; Michel Dumontier; Nico M. Franz; Frank Friedrich; George V. Gkouto; Melissa Haendel; Luke J. Harmon; Terry F. Hayamizu; Yongqun He; Heather M. Hines; Nizar Ibrahim; Laura M. Jackson; Pankaj Jaiswal; Christina James-Zorn; Sebastian Koehler; Guillaume Lecointre; Hilmar Lapp; Carolyn J. Lawrence; Nicolas Le Novere; John G. Lundberg; James Macklin; Austin R. Mast; Peter E. Midford; Istvan Miko; Christopher J. Mungall; Anika Oellrich; David Osumi-Sutherland; Helen Parkinson; Martin J. Ramirez; 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 M. Mabee

doi:10.1371/journal.pbio.1002033

Finding Our Way through Phenotypes

Andrew R. 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, Melanie Courtot, Sandor Csoesz, Hong Cui, Wasila Dahdul, Sandip Das, T. Alexander Dececchi, Agnes Dettai, Rui Diogo, Robert E. DruzinskyMichel Dumontier, Nico M. Franz, Frank Friedrich, George V. Gkouto, Melissa Haendel, Luke J. Harmon, Terry F. Hayamizu, Yongqun He, Heather M. Hines, Nizar Ibrahim, Laura M. Jackson, Pankaj Jaiswal, Christina James-Zorn, Sebastian Koehler, Guillaume Lecointre, Hilmar Lapp, Carolyn J. Lawrence, Nicolas Le Novere, John G. Lundberg, James Macklin, Austin R. Mast, Peter E. Midford, Istvan Miko, Christopher J. Mungall, Anika Oellrich, David Osumi-Sutherland, Helen Parkinson, Martin J. Ramirez, 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 M. Mabee

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

133 Citations (Web of Science)

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
Article number	e1002033
Journal	Plos Biology
Volume	13
Issue number	1
DOIs	https://doi.org/10.1371/journal.pbio.1002033
Publication status	Published - Jan 2015
Externally published	Yes

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10.1371/journal.pbio.1002033

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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., Csoesz, S., Cui, H., Dahdul, W., Das, S., Dececchi, T. A., Dettai, A., Diogo, R., ... Mabee, P. M. (2015). Finding Our Way through Phenotypes. Plos Biology, 13(1), [e1002033]. https://doi.org/10.1371/journal.pbio.1002033

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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.",

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

year = "2015",

month = jan,

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language = "English",

volume = "13",

journal = "Plos Biology",

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publisher = "Public Library of Science",

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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, Csoesz, S, Cui, H, Dahdul, W, Das, S, Dececchi, TA, Dettai, A, Diogo, R, Druzinsky, RE, Dumontier, M, Franz, NM, Friedrich, F, Gkouto, GV, Haendel, M, Harmon, LJ, Hayamizu, TF, He, Y, Hines, HM, Ibrahim, N, Jackson, LM, Jaiswal, P, James-Zorn, C, Koehler, 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, PM 2015, 'Finding Our Way through Phenotypes', Plos Biology, vol. 13, no. 1, e1002033. https://doi.org/10.1371/journal.pbio.1002033

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T1 - Finding Our Way through Phenotypes

AU - Deans, Andrew R.

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, Melanie

AU - Csoesz, Sandor

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 - Gkouto, 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 - Koehler, Sebastian

AU - Lecointre, Guillaume

AU - Lapp, Hilmar

AU - Lawrence, Carolyn J.

AU - Le Novere, 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 - Ramirez, Martin 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 M.

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