Finding our way through phenotypes.

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.

Department

Description

Provenance

Citation

Published Version (Please cite this version)

10.1371/journal.pbio.1002033

Publication Info

Deans, Andrew R, Suzanna E Lewis, Eva Huala, Salvatore S Anzaldo, Michael Ashburner, James P Balhoff, David C Blackburn, Judith A Blake, et al. (2015). Finding our way through phenotypes. PLoS Biol, 13(1). p. e1002033. 10.1371/journal.pbio.1002033 Retrieved from https://hdl.handle.net/10161/10187.

This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.

Scholars@Duke

Wall

Christine Elizabeth Wall

Research Professor Emerita of Evolutionary Anthropology

The focus of my work is the functional and evolutionary anatomy of the head, with an emphasis on how the feeding apparatus works and how it influences and is influenced by other structures and functions. My research focuses primarily on the functional anatomy of extant and extinct primates, but I am also interested in other mammalian groups.

Current research projects include:

(1) a detailed study of the architecture, fiber types, and the recruitment patterns of the jaw adductor muscles of priamtes. The goals are to determine the nature of the general relationship between architecture (e.g., cross-sectional area) and fiber type for the jaw adductors, to find out whether the jaw adductors are sexually dimorphic in these anthropoid primates, to test for co-variation with dietary adaptation, and to develop biomechanical models to describe this relationship and relate it to size, function, and energetic requirements;

(2) investigations of the energetic costs of feeding behaviors in humans and nonhuman primates. The goal of this work is to better understand the relationship between the functional anatomy of the feeding apparatus and the metabolic costs that an animal incurs during feeding.

(3) development of a public database - the Feeding Experiments End-user Database (FEED, www.feedexp.org) in collaboration with Dr. Rebecca German (Johns Hopkins), Dr. Susan Williams (Ohio Univ.), Dr. Chris Vinyard (NEOUCOM), and the National Evolutionary Synthesis Center. This database includes physiological data from a large number of mammalian species collected by numerous researchers. Its design will allow synthetic and integrative analyses of the evolution of the oropharyngeal apparatus and feeding behaviors in mammals. The public instance of FEED is available at https://feedexp.org/  We are also developing new analytical tools for inter-specific comparisons of raw electromyographic recordings that can be used to process data in FEED.


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