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Ramsey J, McIntosh B, Renfro D, Aleksander SA, LaBonte S, Ross C, Zweifel AE, Liles N, Farrar S, Gill JJ, Erill I, Ades S, Berardini TZ, Bennett JA, Brady S, Britton R, Carbon S, Caruso SM, Clements D, Dalia R, Defelice M, Doyle EL, Friedberg I, Gurney SMR, Hughes L, Johnson A, Kowalski JM, Li D, Lovering RC, Mans TL, McCarthy F, Moore SD, Murphy R, Paustian TD, Perdue S, Peterson CN, Prüß BM, Saha MS, Sheehy RR, Tansey JT, Temple L, Thorman AW, Trevino S, Vollmer AC, Walbot V, Willey J, Siegele DA, Hu JC. Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PLoS Comput Biol 2021; 17:e1009463. [PMID: 34710081 PMCID: PMC8553046 DOI: 10.1371/journal.pcbi.1009463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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.
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Affiliation(s)
- Jolene Ramsey
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
- Center for Phage Technology, 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
- Center for Phage Technology, 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
- Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
- Department of Computer Science and Electrical Engineering, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Sarah Ades
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Tanya Z. Berardini
- The Arabidopsis Information Resource, Phoenix Bioinformatics, Newark, California, United States of America
| | - 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
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - 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 Microbiology, Miami University, Oxford, Ohio, United States of America
| | - 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
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - 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, Texas, United States of America
| | - James C. Hu
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
- Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
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