Gramene Pathway Curation Jamboree 7th-10th August, 2018

Dr. Sushma Naithani (Oregon State University) organized a Pathway Curation Jamboree for the Plant Reactome, a portal of the Gramene Database, at the site iof the International Conference on Biological Ontology 2018.  The jamboree took place on August 7-10, 2018 for total 20 hours (4 hours each day). The aim of the jamboree was to introduce plant researchers to curation strategies and tools for curating plant pathways; harness their expertise to curate plant pathways or identify high-quality gene-gene interaction datasets for various plant species that can be made available via web service to Plant Reactome users; and develop a network of biologists for community curation. 

In total, community curators included 5 graduate students, one postdoc, and 1 senior faculty. Also, two faculty members working in non-plants visited and spent time in learning pathway curation strategy. Jamboree participants curated 7 published papers and provided detailed annotations for ~100 genes. The participants also learned to draw plant pathways using PathVisio tool (WikiPathways) and Reactome curator tool.  Interestingly, one graduate student wrote an innovative script to map unique UniProt IDs to rice genes for automated data population. 

The participants working in both the model and non-model organism appreciated jamboree exercise and here are some of their comments

Dr. Kelly Vining, Assistant Professor, Department of Horticulture at Oregon State University:

“The Pathway Jamboree was very useful for learning about available resources for pathway curation. Following the process from literature review to functional annotations showed how heterogeneous available data about specific genes can be, and showed limitations of available genome annotations. For those of us working on non-model organisms, this experience was a good entry point from which we may think about how to apply or cross-reference gene model annotations, and ultimately develop taxon-specific pathway resources.”

Lillian K Padgitt-Cobb, Graduate student, Department of Biochemistry & Biophysics at Oregon State University:

“I work in a non-model species hop (Humulus lupulus). During the Pathway Curation Jamboree, I worked with model species rice and learned how the standardization of gene names is critical for pathway mapping. I attained a better sense of how different sources of evidence complement each other, and how to proceed forward when not all sources of evidence are available. I found it very useful to draw diagrams to begin the process of mapping pathways and to learn about Reactome Curator Tool. This exercise provided me framework to work with hop genes annotations and build genomic resources for the non-model plant species.”

Priya Garg, Oregon State University:

"I really liked the jamboree this time as this was more structured and detailed version of the curation process training. We were facilitated with a personalized guidance to go through the complex process of the curation of developmental pathways. The sessions were more streamlined and I really liked the approach to start with an overview of the whole workflow and then to proceed with the details of each of data entry points, mentioned in the workflow. It actually provided a deeper understanding of the curation pipeline at granular level."

Valerie Fraser, Graduate student, Department of Botany and Plant Pathology at Oregon State University:

“During the Jamboree, I spent approximately 7 hours each day learning about and working on curation for plant pathways and curated endosperm development pathway consisting of 30 genes from 2 published articles. I learned about the curation process and about several tools available that make curation and visualization of gene data less complicated than it sounds. Much of what I learned here will be useful for my own research down the road, and the interpersonal connections I made here are already beneficial for me.”