The digital revolution in phenotyping

Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo Georgiev, Hongfang D Liu, Kevin Livingston, Augustin Luna, Ann Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, definei as observable characteristics of organisms, can be seen as one of the bridges that lead to a translation of experimental findings into clinical applications and thereby support 'bench to bedside' efforts. However, to build this translational bridge, a common and universal understanding of phenotypes is required that goes beyond domain-specific definitions. To achieve this ambitious goal, a digital revolution is ongoing that enables the encoding of data in computer-readable formats and the data storage in specialized repositories, ready for integration, enabling translational research. While phenome research is an ongoing endeavor, the true potential hidden in the currently available data still needs to be unlocked, offering exciting opportunities for the forthcoming years. Here, we provide insights into the state-of-the-art in digital phenotyping, bymea of representing, acquiring and analyzing phenotype data. In addition, we provide visions of this field for future research work that could enable better applications of phenotype data.

Original languageEnglish (US)
Pages (from-to)819-830
Number of pages12
JournalBriefings in Bioinformatics
Volume17
Issue number5
DOIs
StatePublished - Sep 1 2016

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Phenotype
Genes
Translational Medical Research
Information Storage and Retrieval
Pharmacogenetics
Genetic Association Studies
Data storage equipment
Drug Discovery
Research

Keywords

  • Acquisition
  • Interoperability
  • Knowledge discovery
  • Phenomics
  • Phenotypes
  • Semantic representation

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

Cite this

Oellrich, A., Collier, N., Groza, T., Rebholz-Schuhmann, D., Shah, N., Bodenreider, O., ... Dumontier, M. (2016). The digital revolution in phenotyping. Briefings in Bioinformatics, 17(5), 819-830. https://doi.org/10.1093/bib/bbv083

The digital revolution in phenotyping. / Oellrich, Anika; Collier, Nigel; Groza, Tudor; Rebholz-Schuhmann, Dietrich; Shah, Nigam; Bodenreider, Olivier; Boland, Mary Regina; Georgiev, Ivo; Liu, Hongfang D; Livingston, Kevin; Luna, Augustin; Mallon, Ann Marie; Manda, Prashanti; Robinson, Peter N.; Rustici, Gabriella; Simon, Michelle; Wang, Liqin; Winnenburg, Rainer; Dumontier, Michel.

In: Briefings in Bioinformatics, Vol. 17, No. 5, 01.09.2016, p. 819-830.

Research output: Contribution to journalArticle

Oellrich, A, Collier, N, Groza, T, Rebholz-Schuhmann, D, Shah, N, Bodenreider, O, Boland, MR, Georgiev, I, Liu, HD, Livingston, K, Luna, A, Mallon, AM, Manda, P, Robinson, PN, Rustici, G, Simon, M, Wang, L, Winnenburg, R & Dumontier, M 2016, 'The digital revolution in phenotyping', Briefings in Bioinformatics, vol. 17, no. 5, pp. 819-830. https://doi.org/10.1093/bib/bbv083
Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O et al. The digital revolution in phenotyping. Briefings in Bioinformatics. 2016 Sep 1;17(5):819-830. https://doi.org/10.1093/bib/bbv083
Oellrich, Anika ; Collier, Nigel ; Groza, Tudor ; Rebholz-Schuhmann, Dietrich ; Shah, Nigam ; Bodenreider, Olivier ; Boland, Mary Regina ; Georgiev, Ivo ; Liu, Hongfang D ; Livingston, Kevin ; Luna, Augustin ; Mallon, Ann Marie ; Manda, Prashanti ; Robinson, Peter N. ; Rustici, Gabriella ; Simon, Michelle ; Wang, Liqin ; Winnenburg, Rainer ; Dumontier, Michel. / The digital revolution in phenotyping. In: Briefings in Bioinformatics. 2016 ; Vol. 17, No. 5. pp. 819-830.
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