Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Journal: PLoS computational biology
PMID: 34710081

Abstract

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

Authors

  • Jolene Ramsey
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Brenley McIntosh
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Daniel Renfro
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Suzanne A Aleksander
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Sandra LaBonte
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Curtis Ross
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Adrienne E Zweifel
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Nathan Liles
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Shabnam Farrar
    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America.
  • Jason J Gill
    Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America.
  • Ivan Erill
    Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
  • Sarah Ades
    Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America.
  • Tanya Z Berardini
    Arabidopsis Information Resource, Phoenix Bioinformatics, Redwood City, CA 94063, USA.
  • Jennifer A Bennett
    Department of Biology and Earth Science, Otterbein University, Westerville, Ohio, United States of America.
  • Siobhan Brady
    Department of Plant Biology and Genome Center, University of California Davis, Davis, California, United States of America.
  • Robert Britton
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America.
  • Seth Carbon
    Berkeley Bioinformatics Open-Source Projects, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd. MS 977, Berkeley, CA, 94720, USA.
  • Steven M Caruso
    Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America.
  • Dave Clements
    Department of Biology, John Hopkins University, Baltimore, Maryland, United States of America.
  • Ritu Dalia
    Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America.
  • Meredith Defelice
    Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America.
  • Erin L Doyle
    Biology Department, Doane University, Crete, Nebraska, United States of America.
  • Iddo Friedberg
    Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.
  • Susan M R Gurney
    Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America.
  • Lee Hughes
    Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America.
  • Allison Johnson
    Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America.
  • Jason M Kowalski
    Biological Sciences Department, University of Wisconsin-Parkside, Kenosha, Wisconsin, United States of America.
  • Donghui Li
    The Arabidopsis Information Resource, Phoenix Bioinformatics, Newark, California, United States of America.
  • Ruth C Lovering
    Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London, WC1E 6JF, UK. r.lovering@ucl.ac.uk.
  • Tamara L Mans
    Department of Biochemistry and Biotechnology, Minnesota State University Moorhead, Brooklyn Park, Minnesota, United States of America.
  • Fiona McCarthy
    Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America.
  • Sean D Moore
    Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America.
  • Rebecca Murphy
    Department of Biology, Centenary College of Louisiana, Shreveport, Louisiana, United States of America.
  • Timothy D Paustian
    Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America.
  • Sarah Perdue
    Biological Sciences Department, University of Wisconsin-Parkside, Kenosha, Wisconsin, United States of America.
  • Celeste N Peterson
    Biology Department, Suffolk University, Boston, Massachusetts, United States of America.
  • Birgit M Prüß
    Microbiological Sciences Department, North Dakota State University, Fargo, North Dakota, United States of America.
  • Margaret S Saha
    Department of Biology, College of William & Mary, Williamsburg, Virginia, United States of America.
  • Robert R Sheehy
    Biology Department, Radford University, Radford, Virginia, United States of America.
  • John T Tansey
    Department of Biochemistry and Molecular Biology, Otterbein University, Westerville, Ohio, United States of America.
  • Louise Temple
    School of Integrated Sciences, James Madison University, Harrisonburg, Virginia, United States of America.
  • Alexander William Thorman
    Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America.
  • Saul Trevino
    Department of Chemistry, Math, and Physics, Houston Baptist University, Houston, Texas, United States of America.
  • Amy Cheng Vollmer
    Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America.
  • Virginia Walbot
    Department of Biology, Stanford University, Stanford, California, United States of America.
  • Joanne Willey
    Department of Science Education, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, United States of America.
  • Deborah A Siegele
    Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
  • James C Hu
    Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX, 77843, USA.

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