Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)
Authors: Ramsey Jolene , McIntosh Brenley , Renfro Daniel , Aleksander Suzanne A. , LaBonte Sandra , Ross Curtis , Zweifel Adrienne E. , Liles Nathan , Farrar Shabnam , Gill Jason J. , Erill Ivan , Ades Sarah , Berardini Tanya Z. , Bennett Jennifer A. , Brady Siobhan , Britton Robert , Carbon Seth , Caruso Steven M. , Clements Dave , Dalia Ritu , Defelice Meredith , Doyle Erin L. , Friedberg Iddo , Gurney Susan M.R. , Hughes Lee , Johnson Allison , Kowalski Jason M. , Li Donghui , Lovering Ruth C. , Mans Tamara L. , McCarthy Fiona , Moore Sean D. , Murphy Rebecca , Paustian Timothy D. , Perdue Sarah , Peterson Celeste N. , Prüß Birgit M. , Saha Margaret S. , Sheehy Robert R. , Tansey John T. , Temple Louise , Thorman Alexander William , Trevino Saul , Vollmer Amy Cheng , Walbot Virginia , Willey Joanne , Siegele Deborah A. , Hu James C. 
Published: May 2021

Experimental data about known 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 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-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.

Significance Statement

The primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.