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PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

Finding our way through phenotypes.

Author information

1
Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America.
2
Genome Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
3
Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America; Phoenix Bioinformatics, Palo Alto, California, United States of America.
4
School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.
5
Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
6
National Evolutionary Synthesis Center, Durham, North Carolina, United States of America.
7
Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California, United States of America.
8
The Jackson Laboratory, Bar Harbor, Maine, United States of America.
9
Department of Biology, University of Florida, Gainesville, Florida, United States of America.
10
Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France.
11
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
12
Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada.
13
MTA-ELTE-MTM, Ecology Research Group, Pázmány Péter sétány 1C, Budapest, Hungary.
14
School of Information Resources and Library Science, University of Arizona, Tucson, Arizona, United States of America.
15
Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.
16
Department of Botany, University of Delhi, Delhi, India.
17
Department of Anatomy, Howard University College of Medicine, Washington D.C., United States of America.
18
Department of Oral Biology, College of Dentistry, University of Illinois, Chicago, Illinois, United States of America.
19
Stanford Center for Biomedical Informatics Research, Stanford, California, United States of America.
20
Biocenter Grindel and Zoological Museum, Hamburg University, Hamburg, Germany.
21
Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
22
Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, Oregon, United States of America.
23
Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America.
24
Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine, United States of America.
25
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
26
Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America.
27
Cincinnati Children's Hospital, Division of Developmental Biology, Cincinnati, Ohio, United States of America.
28
Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
29
Department of Genetics, Development and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa, United States of America.
30
Signalling ISP, Babraham Institute, Babraham, Cambridgeshire, UK.
31
Department of Ichthyology, The Academy of Natural Sciences, Philadelphia, Pennsylvania, United States of America.
32
Eastern Cereal and Oilseed Research Centre, Ottawa, Ontario, Canada.
33
Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.
34
Richmond, Virginia, United States of America.
35
European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
36
Division of Arachnology, Museo Argentino de Ciencias Naturales - CONICET, Buenos Aires, Argentina.
37
Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, Rostock, Germany.
38
Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin, Berlin, Germany.
39
School of Dental Medicine, University at Buffalo, Buffalo, New York, United States of America.
40
Smithsonian Institution, National Museum of Natural History, Washington, D.C., United States of America.
41
Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, United States of America.
42
Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America.
43
Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America.
44
Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America.
45
Department of Philosophy, University at Buffalo, Buffalo, New York, United States of America.
46
Department of Plant and Microbial Biology, Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California, United States of America.
47
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
48
Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
49
The Data Detektiv, 1412 Stearns Hill Road, Waltham, Massachusetts, United States of America.
50
Canadian National Collection of Insects, Ottawa, Ontario, Canada.
51
Department of Experimental Medical Science, Lund University, Lund, Sweden.
52
Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
53
Universität Bonn, Institut für Evolutionsbiologie und Ökologie, Bonn, Germany.
54
Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America.
55
iPlant Collaborative University of Arizona, Thomas J. Keating Bioresearch Building, Tucson, Arizona, United States of America.
56
Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America.
57
Department of Entomology, Texas A & M University, College, Station, Texas, United States of America.
58
Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America.

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.

PMID:
25562316
PMCID:
PMC4285398
DOI:
10.1371/journal.pbio.1002033
[Indexed for MEDLINE]
Free PMC Article
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