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, defined 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, by means 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.
Highlights
Phenotypes are broadly defined as observable characteristics of organisms and have gained great importance since the discovery of the causative relationship between a given underlying genetic mechanism and its phenotypic manifestation
The increasing development and exploitation of phenotypes has led to a varied range of applications: identifying disease genes [5,6,7,8,9] and characterizing functionally yet unclassified genes [10,11,12], repurposing drugs [13, 14], pharmacogenomics [15,16,17] and pharmacovigilance [18], as well as solving evolutionary questions [19, 20]
This work presents visions for the coming years in phenomics research, as it derives a series of open challenges, based on input collected from the community
Summary
Phenotypes are broadly defined as observable characteristics of organisms and have gained great importance since the discovery of the causative relationship between a given underlying genetic mechanism (e.g. gene expression levels, mutations) and its phenotypic manifestation. With the abundance and ever-increasing amount of data, the ultimate goal is to build a uniform and consistent computer-readable representation, one that enables a seamless collection and integration of phenotypes recorded in biological studies, as well as in a clinical environment.
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