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

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Date
28/10/2021
Author
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
Bennet, JA
Brady, S
Britton, R
Carbon, S
Caruso, SM
Clements, D
Dalia, R
Defelice, M
Doyle, EL
Friedberg, I
Gurney, Susan Margaret Robertson
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, R
Willey, J
Siegele, DA
Hu, JC
Keywords
LB2300 Higher Education
QA75 Electronic computers. Computer science
QH426 Genetics
DAS
MCC
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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.
Citation
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 , Bennet , JA , Brady , S , Britton , R , Carbon , S , Caruso , SM , Clements , D , Dalia , R , Defelice , M , Doyle , EL , Friedberg , I , Gurney , S M R , 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 , R , Willey , J , Siegele , DA & Hu , JC 2021 , ' Crowdsourcing biocuration : the Community Assessment of Community Annotation with Ontologies (CACAO) ' , PLoS Computational Biology , vol. 17 , no. 10 , e1009463 . https://doi.org/10.1371/journal.pcbi.1009463
Publication
PLoS Computational Biology
Status
Non peer reviewed
DOI
https://doi.org/10.1371/journal.pcbi.1009463
ISSN
1553-734X
Type
Journal article
Rights
Copyright: © 2021 Ramsey et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Description
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.
Collections
  • University of St Andrews Research
URI
http://hdl.handle.net/10023/26649

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