Biocuration of rice genes and pathways by OSU undergraduates

Plant Reactome is the pathway portal of Gramene knowledgebase.We combine manual biocuration and gene-orthology based automated projections to provide conceptual framework of system-level plant pathway networks for 106 species of photoautotrophs, including models, crops and species of evolutionary interests. We use rice (Oryza sativa) as a reference species and implement biocuration to improve the functional annotation of genes, and to construct gene-networks and pathways. In these efforts, we engage undergraduate students in small research projects designed to develop their genomic data literacy by leveraging affiliated bioinformatics data science courses, thesis projects, research programs, and experiential learning internships—all available at Oregon State University (OSU). In the winter and spring terms of 2021, six students worked under the supervision of Dr. Sushma NaithaniDepartment of Botany and Plant Pathology at OSU. These undergraduate students contributed to biocuration of gene-networks involved in abiotic stress response based on published scientific literature, and analyses of transcriptome datasets. 

The student projects were funded by the Undergraduate Research, Scholarship and the Arts (URSA) Engage Program at Oregon State University.   

Learn about our 2021 biocuration research stories by watching the following 3 minutes flash talks, also available from Gramene’s YouTube channel  

Biocuration flash talks by Oregon State University undergraduates

Quentin Beers (Freshman, Biochemistry and Molecular Biology Major), worked on the biocuration of rice gene network involved in drought response

Sarah El-Husseini (Sophomore, Bio-Health Science Major), worked on stress response to salinity in Oryza sativa

Madeline Goebel (Sophomore, Biochemistry and Molecular Biology Major) pursued the project, Biocuration of heat response pathway in rice

Olivia Worley (Sophomore, Biochemistry and Molecular Biology Major) did the bicuration of common transcription hubs and networks involved in ABA, salinity, cold and drought response in rice 

Gwendolyn Michna (Sophomore, Biochemistry and Molecular Biology Major) did her project on genes involved in submergence response in rice  

Amitavo Ganguli (Junior, Geography & Geospatial Science Major, Minor in Biology) developed software applications for mining the Plant Reactome database for the evolutionary history of metabolic pathways