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

Simple item page
dc.contributor.authorRamsey, Joleneen
dc.contributor.authorMcIntosh, Brenleyen
dc.contributor.authorRenfro, Danielen
dc.contributor.authorAleksander, Suzanne A.en
dc.contributor.authorLaBonte, Sandraen
dc.contributor.authorRoss, Curtisen
dc.contributor.authorZweifel, Adrienne E.en
dc.contributor.authorLiles, Nathanen
dc.contributor.authorFarrar, Shabnamen
dc.contributor.authorGill, Jason J.en
dc.contributor.authorErill, Ivanen
dc.contributor.authorAdes, Sarahen
dc.contributor.authorBerardini, Tanya Z.en
dc.contributor.authorBennett, Jennifer A.en
dc.contributor.authorBrady, Siobhanen
dc.contributor.authorBritton, Roberten
dc.contributor.authorCarbon, Sethen
dc.contributor.authorCaruso, Steven M.en
dc.contributor.authorClements, Daveen
dc.contributor.authorDalia, Rituen
dc.contributor.authorDefelice, Meredithen
dc.contributor.authorDoyle, Erin L.en
dc.contributor.authorFriedberg, Iddoen
dc.contributor.authorGurney, Susan M. R.en
dc.contributor.authorHughes, Leeen
dc.contributor.authorJohnson, Allisonen
dc.contributor.authorKowalski, Jason M.en
dc.contributor.authorLi, Donghuien
dc.contributor.authorLovering, Ruth C.en
dc.contributor.authorMans, Tamara L.en
dc.contributor.authorMcCarthy, Fionaen
dc.contributor.authorMoore, Sean D.en
dc.contributor.authorMurphy, Rebeccaen
dc.contributor.authorPaustian, Timothy D.en
dc.contributor.authorPerdue, Sarahen
dc.contributor.authorPeterson, Celeste N.en
dc.contributor.authorPruss, Birgit M.en
dc.contributor.authorSaha, Margaret S.en
dc.contributor.authorSheehy, Robert R.en
dc.contributor.authorTansey, John T.en
dc.contributor.authorTemple, Louiseen
dc.contributor.authorThorman, Alexander Williamen
dc.contributor.authorTrevino, Saulen
dc.contributor.authorVollmer, Amy Chengen
dc.contributor.authorWalbot, Virginiaen
dc.contributor.authorWilley, Joanneen
dc.contributor.authorSiegele, Deborah A.en
dc.contributor.authorHu, James C.en
dc.date.accessioned2022-03-29T12:17:00Zen
dc.date.available2022-03-29T12:17:00Zen
dc.date.issued2021-10en
dc.description.abstractAuthor summary 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 (GO) 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, represent the best return on investment by improving data accessibility across the biological sciences and allowing novel insights between evolutionarily related organisms. To supplement professional curation, our Community Assessment of Community Annotation with Ontologies (CACAO) project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in the contribution of thousands of unique, validated entries to public resources. Importantly, the annotations described here initiated by nonexperts often deal with topics not typically covered by the experts. These annotations are now being used by scientists worldwide in their research efforts.</p> 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.</p>en
dc.description.notesFunding: Funding was provided by the National Institutes of Health (awards GM088849 and GM089636 to J.C.H.) and the National Science Foundation (awards EF-0949351 and DBI-1565146 to J.C.H.). S.C. was supported by the Director, Office of Science, Office of Basic Energy Science, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.description.sponsorshipNational Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [GM088849, GM089636]; National Science FoundationNational Science Foundation (NSF) [EF-0949351, DBI-1565146]; Office of Science, Office of Basic Energy Science, of the U.S. Department of EnergyUnited States Department of Energy (DOE) [DE-AC02-05CH11231]en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1371/journal.pcbi.1009463en
dc.identifier.eissn1553-7358en
dc.identifier.issn1553-734Xen
dc.identifier.issue10en
dc.identifier.othere1009463en
dc.identifier.pmid34710081en
dc.identifier.urihttp://hdl.handle.net/10919/109480en
dc.identifier.volume17en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleCrowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)en
dc.title.serialPlos Computational Biologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
journal.pcbi.1009463.pdf
Size:
1.4 MB
Format:
Adobe Portable Document Format
Description:
Published version
Download

Collections

Advanced Research Computing