Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)
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....
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2021
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Biology (General) QH301-705.5 |
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Biology (General) QH301-705.5 Jolene Ramsey Brenley McIntosh Daniel Renfro Suzanne A. Aleksander Sandra LaBonte Curtis Ross Adrienne E. Zweifel Nathan Liles Shabnam Farrar Jason J. Gill Ivan Erill Sarah Ades Tanya Z. Berardini Jennifer A. Bennett Siobhan Brady Robert Britton Seth Carbon Steven M. Caruso Dave Clements Ritu Dalia Meredith Defelice Erin L. Doyle Iddo Friedberg Susan M. R. Gurney Lee Hughes Allison Johnson Jason M. Kowalski Donghui Li Ruth C. Lovering Tamara L. Mans Fiona McCarthy Sean D. Moore Rebecca Murphy Timothy D. Paustian Sarah Perdue Celeste N. Peterson Birgit M. Prüß Margaret S. Saha Robert R. Sheehy John T. Tansey Louise Temple Alexander William Thorman Saul Trevino Amy Cheng Vollmer Virginia Walbot Joanne Willey Deborah A. Siegele James C. Hu Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) |
| description |
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. Author 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. |
| format |
article |
| author |
Jolene Ramsey Brenley McIntosh Daniel Renfro Suzanne A. Aleksander Sandra LaBonte Curtis Ross Adrienne E. Zweifel Nathan Liles Shabnam Farrar Jason J. Gill Ivan Erill Sarah Ades Tanya Z. Berardini Jennifer A. Bennett Siobhan Brady Robert Britton Seth Carbon Steven M. Caruso Dave Clements Ritu Dalia Meredith Defelice Erin L. Doyle Iddo Friedberg Susan M. R. Gurney Lee Hughes Allison Johnson Jason M. Kowalski Donghui Li Ruth C. Lovering Tamara L. Mans Fiona McCarthy Sean D. Moore Rebecca Murphy Timothy D. Paustian Sarah Perdue Celeste N. Peterson Birgit M. Prüß Margaret S. Saha Robert R. Sheehy John T. Tansey Louise Temple Alexander William Thorman Saul Trevino Amy Cheng Vollmer Virginia Walbot Joanne Willey Deborah A. Siegele James C. Hu |
| author_facet |
Jolene Ramsey Brenley McIntosh Daniel Renfro Suzanne A. Aleksander Sandra LaBonte Curtis Ross Adrienne E. Zweifel Nathan Liles Shabnam Farrar Jason J. Gill Ivan Erill Sarah Ades Tanya Z. Berardini Jennifer A. Bennett Siobhan Brady Robert Britton Seth Carbon Steven M. Caruso Dave Clements Ritu Dalia Meredith Defelice Erin L. Doyle Iddo Friedberg Susan M. R. Gurney Lee Hughes Allison Johnson Jason M. Kowalski Donghui Li Ruth C. Lovering Tamara L. Mans Fiona McCarthy Sean D. Moore Rebecca Murphy Timothy D. Paustian Sarah Perdue Celeste N. Peterson Birgit M. Prüß Margaret S. Saha Robert R. Sheehy John T. Tansey Louise Temple Alexander William Thorman Saul Trevino Amy Cheng Vollmer Virginia Walbot Joanne Willey Deborah A. Siegele James C. Hu |
| author_sort |
Jolene Ramsey |
| title |
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) |
| title_short |
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) |
| title_full |
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) |
| title_fullStr |
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) |
| title_full_unstemmed |
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) |
| title_sort |
crowdsourcing biocuration: the community assessment of community annotation with ontologies (cacao) |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2021 |
| url |
https://doaj.org/article/e1b8e037e5fb463fad2c0350fb2083e1 |
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oai:doaj.org-article:e1b8e037e5fb463fad2c0350fb2083e12021-11-04T05:44:47ZCrowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)1553-734X1553-7358https://doaj.org/article/e1b8e037e5fb463fad2c0350fb2083e12021-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8553046/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Experimental 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. Author 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.Jolene RamseyBrenley McIntoshDaniel RenfroSuzanne A. AleksanderSandra LaBonteCurtis RossAdrienne E. ZweifelNathan LilesShabnam FarrarJason J. GillIvan ErillSarah AdesTanya Z. BerardiniJennifer A. BennettSiobhan BradyRobert BrittonSeth CarbonSteven M. CarusoDave ClementsRitu DaliaMeredith DefeliceErin L. DoyleIddo FriedbergSusan M. R. GurneyLee HughesAllison JohnsonJason M. KowalskiDonghui LiRuth C. LoveringTamara L. MansFiona McCarthySean D. MooreRebecca MurphyTimothy D. PaustianSarah PerdueCeleste N. PetersonBirgit M. PrüßMargaret S. SahaRobert R. SheehyJohn T. TanseyLouise TempleAlexander William ThormanSaul TrevinoAmy Cheng VollmerVirginia WalbotJoanne WilleyDeborah A. SiegeleJames C. HuPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 10 (2021) |