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PLoS Biol 2015 Jan 06;131:e1002033. doi: 10.1371/journal.pbio.1002033.
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Finding Our Way through Phenotypes.

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 .

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.

PubMed ID: 25562316
PMC ID: PMC4285398
Article link: PLoS Biol
Grant support: [+]

Species referenced: Xenopus
Genes referenced: actl6a ids myb plxnd1

Article Images: [+] show captions
References [+] :
Aboelkassem, Selective pumping in a network: insect-style microscale flow transport. 2013, Pubmed