title: 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.
authors.affiliation: Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Deans
authors.affiliation: Genome Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
authors.affiliation: Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America; Phoenix Bioinformatics, Palo Alto, California, United States of America.
authors.forename: Eva
authors.initials: E
authors.lastname: Huala
authors.affiliation: School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: Salvatore S
authors.initials: SS
authors.lastname: Anzaldo
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Michael
authors.initials: M
authors.lastname: Ashburner
authors.affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, United States of America.
authors.forename: James P
authors.initials: JP
authors.lastname: Balhoff
authors.affiliation: Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California, United States of America.
authors.forename: David C
authors.initials: DC
authors.lastname: Blackburn
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine, United States of America.
authors.forename: Judith A
authors.initials: JA
authors.lastname: Blake
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida, United States of America.
authors.forename: J Gordon
authors.initials: JG
authors.lastname: Burleigh
authors.affiliation: Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Chanet
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Laurel D
authors.initials: LD
authors.lastname: Cooper
authors.affiliation: Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Courtot
authors.affiliation: MTA-ELTE-MTM, Ecology Research Group, Pázmány Péter sétány 1C, Budapest, Hungary.
authors.forename: Sándor
authors.initials: S
authors.lastname: Csösz
authors.affiliation: School of Information Resources and Library Science, University of Arizona, Tucson, Arizona, United States of America.
authors.forename: Hong
authors.initials: H
authors.lastname: Cui
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.
authors.forename: Wasila
authors.initials: W
authors.lastname: Dahdul
authors.affiliation: Department of Botany, University of Delhi, Delhi, India.
authors.forename: Sandip
authors.initials: S
authors.lastname: Das
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.
authors.forename: T Alexander
authors.initials: TA
authors.lastname: Dececchi
authors.affiliation: Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France.
authors.forename: Agnes
authors.initials: A
authors.lastname: Dettai
authors.affiliation: Department of Anatomy, Howard University College of Medicine, Washington D.C., United States of America.
authors.forename: Rui
authors.initials: R
authors.lastname: Diogo
authors.affiliation: Department of Oral Biology, College of Dentistry, University of Illinois, Chicago, Illinois, United States of America.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Druzinsky
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford, California, United States of America.
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.affiliation: School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: Nico M
authors.initials: NM
authors.lastname: Franz
authors.affiliation: Biocenter Grindel and Zoological Museum, Hamburg University, Hamburg, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Friedrich
authors.affiliation: Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
authors.forename: George V
authors.initials: GV
authors.lastname: Gkoutos
authors.affiliation: Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, Oregon, United States of America.
authors.forename: Melissa
authors.initials: M
authors.lastname: Haendel
authors.affiliation: Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America.
authors.forename: Luke J
authors.initials: LJ
authors.lastname: Harmon
authors.affiliation: Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine, United States of America.
authors.forename: Terry F
authors.initials: TF
authors.lastname: Hayamizu
authors.affiliation: 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.
authors.forename: Yongqun
authors.initials: Y
authors.lastname: He
authors.affiliation: Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America.
authors.forename: Heather M
authors.initials: HM
authors.lastname: Hines
authors.affiliation: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Nizar
authors.initials: N
authors.lastname: Ibrahim
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.
authors.forename: Laura M
authors.initials: LM
authors.lastname: Jackson
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
authors.affiliation: Cincinnati Children's Hospital, Division of Developmental Biology, Cincinnati, Ohio, United States of America.
authors.forename: Christina
authors.initials: C
authors.lastname: James-Zorn
authors.affiliation: Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Köhler
authors.affiliation: Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Lecointre
authors.affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, United States of America.
authors.forename: Hilmar
authors.initials: H
authors.lastname: Lapp
authors.affiliation: Department of Genetics, Development and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Carolyn J
authors.initials: CJ
authors.lastname: Lawrence
authors.affiliation: Signalling ISP, Babraham Institute, Babraham, Cambridgeshire, UK.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Le Novère
authors.affiliation: Department of Ichthyology, The Academy of Natural Sciences, Philadelphia, Pennsylvania, United States of America.
authors.forename: John G
authors.initials: JG
authors.lastname: Lundberg
authors.affiliation: Eastern Cereal and Oilseed Research Centre, Ottawa, Ontario, Canada.
authors.forename: James
authors.initials: J
authors.lastname: Macklin
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.
authors.forename: Austin R
authors.initials: AR
authors.lastname: Mast
authors.affiliation: Richmond, Virginia, United States of America.
authors.forename: Peter E
authors.initials: PE
authors.lastname: Midford
authors.affiliation: Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America.
authors.forename: István
authors.initials: I
authors.lastname: Mikó
authors.affiliation: Genome Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
authors.affiliation: European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
authors.forename: Anika
authors.initials: A
authors.lastname: Oellrich
authors.affiliation: European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Osumi-Sutherland
authors.affiliation: European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.affiliation: Division of Arachnology, Museo Argentino de Ciencias Naturales - CONICET, Buenos Aires, Argentina.
authors.forename: Martín J
authors.initials: MJ
authors.lastname: Ramírez
authors.affiliation: Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, Rostock, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Richter
authors.affiliation: Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin, Berlin, Germany.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Robinson
authors.affiliation: School of Dental Medicine, University at Buffalo, Buffalo, New York, United States of America.
authors.forename: Alan
authors.initials: A
authors.lastname: Ruttenberg
authors.affiliation: Smithsonian Institution, National Museum of Natural History, Washington, D.C., United States of America.
authors.forename: Katja S
authors.initials: KS
authors.lastname: Schulz
authors.affiliation: Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, United States of America.
authors.forename: Erik
authors.initials: E
authors.lastname: Segerdell
authors.affiliation: Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America.
authors.forename: Katja C
authors.initials: KC
authors.lastname: Seltmann
authors.affiliation: Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sharkey
authors.affiliation: Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America.
authors.forename: Aaron D
authors.initials: AD
authors.lastname: Smith
authors.affiliation: Department of Philosophy, University at Buffalo, Buffalo, New York, United States of America.
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
authors.affiliation: Department of Plant and Microbial Biology, Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California, United States of America.
authors.forename: Chelsea D
authors.initials: CD
authors.lastname: Specht
authors.affiliation: 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.
authors.forename: R Burke
authors.initials: RB
authors.lastname: Squires
authors.affiliation: Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Thacker
authors.affiliation: The Data Detektiv, 1412 Stearns Hill Road, Waltham, Massachusetts, United States of America.
authors.forename: Anne
authors.initials: A
authors.lastname: Thessen
authors.affiliation: Canadian National Collection of Insects, Ottawa, Ontario, Canada.
authors.forename: Jose
authors.initials: J
authors.lastname: Fernandez-Triana
authors.affiliation: Department of Experimental Medical Science, Lund University, Lund, Sweden.
authors.forename: Mauno
authors.initials: M
authors.lastname: Vihinen
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Vize
authors.affiliation: Universität Bonn, Institut für Evolutionsbiologie und Ökologie, Bonn, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Vogt
authors.affiliation: Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America.
authors.forename: Christine E
authors.initials: CE
authors.lastname: Wall
authors.affiliation: iPlant Collaborative University of Arizona, Thomas J. Keating Bioresearch Building, Tucson, Arizona, United States of America.
authors.forename: Ramona L
authors.initials: RL
authors.lastname: Walls
authors.affiliation: Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America.
authors.forename: Monte
authors.initials: M
authors.lastname: Westerfeld
authors.affiliation: Department of Entomology, Texas A & M University, College, Station, Texas, United States of America.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Wharton
authors.affiliation: Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, Rostock, Germany.
authors.forename: Christian S
authors.initials: CS
authors.lastname: Wirkner
authors.affiliation: Department of Entomology, Texas A & M University, College, Station, Texas, United States of America.
authors.forename: James B
authors.initials: JB
authors.lastname: Woolley
authors.affiliation: Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Yoder
authors.affiliation: Cincinnati Children's Hospital, Division of Developmental Biology, Cincinnati, Ohio, United States of America.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Zorn
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.
authors.forename: Paula
authors.initials: P
authors.lastname: Mabee
mesh_terms: D000818:Animals; D019295:Computational Biology; D066289:Data Curation; D016208:Databases, Factual / Q000592:standards; D059647:Gene-Environment Interaction; D056726:Genetic Association Studies; D023281:Genomics; D006801:Humans; D010641:Phenotype; D012015:Reference Standards; D015203:Reproducibility of Results; D009626:Terminology as Topic