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Finding our way through phenotypes.

Publication ,  Journal Article
Deans, AR; Lewis, SE; Huala, E; Anzaldo, SS; Ashburner, M; Balhoff, JP; Blackburn, DC; Blake, JA; Burleigh, JG; Chanet, B; Cooper, LD; Cui, H ...
Published in: PLoS biology
January 2015

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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Published In

PLoS biology

DOI

EISSN

1545-7885

ISSN

1544-9173

Publication Date

January 2015

Volume

13

Issue

1

Start / End Page

e1002033

Related Subject Headings

  • Terminology as Topic
  • Reproducibility of Results
  • Reference Standards
  • Phenotype
  • Humans
  • Genomics
  • Genetic Association Studies
  • Gene-Environment Interaction
  • Developmental Biology
  • Databases, Factual
 

Citation

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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), e1002033. https://doi.org/10.1371/journal.pbio.1002033
Deans, Andrew R., Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, et al. “Finding our way through phenotypes.PLoS Biology 13, no. 1 (January 2015): e1002033. https://doi.org/10.1371/journal.pbio.1002033.
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, et al. Finding our way through phenotypes. PLoS biology. 2015 Jan;13(1):e1002033.
Deans, Andrew R., et al. “Finding our way through phenotypes.PLoS Biology, vol. 13, no. 1, Jan. 2015, p. e1002033. Epmc, doi:10.1371/journal.pbio.1002033.
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, Mikó 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. Finding our way through phenotypes. PLoS biology. 2015 Jan;13(1):e1002033.
Journal cover image

Published In

PLoS biology

DOI

EISSN

1545-7885

ISSN

1544-9173

Publication Date

January 2015

Volume

13

Issue

1

Start / End Page

e1002033

Related Subject Headings

  • Terminology as Topic
  • Reproducibility of Results
  • Reference Standards
  • Phenotype
  • Humans
  • Genomics
  • Genetic Association Studies
  • Gene-Environment Interaction
  • Developmental Biology
  • Databases, Factual