Involving community in genes and pathway curation.

Sushma Naithani,Kelly Vining,Parul Gupta,Justin Preece,Lillian K Padgitt-Cobb,Matthew Martin,Valerie Fraser,Pankaj Jaiswal,Priyanka Garg

doi:10.1093/database/bay146

Sushma Naithani, Kelly Vining + Show 7 more

Open Access

https://doi.org/10.1093/database/bay146

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Abstract

Biocuration plays a crucial role in building databases and complex systems-level platforms required for processing, annotating and analyzing ‘Big Data’ in biology. However, biocuration efforts cannot keep pace with a dramatic increase in the production of omics data; this presents one of the bottlenecks in genomics. In two pathway curation jamborees, Plant Reactome curators tested strategies for introducing researchers to pathway curation tools, harnessing biologists’ expertise in curating plant pathways and developing a network of community biocurators. We summarize the strategy, workflow and outcomes of these exercises, and discuss the role of community biocuration in advancing databases and genomic resources.

Highlights

Big data generation in biology is becoming easier, cheaper and faster
These systems-level platforms such as Ensembl–Gramene [1], Phytozome [2], Kyoto Encyclopedia of Genes and Genomes (KEGG) [3], Reactome [4], Plant Reactome [5], BioCyc [6] and speciesspecific metabolic networks [i.e. Plant Metabolic Network [7], RiceCyc [8], MaizeCyc [9], VitisCyc [10], FragariaCyc [11], etc.] allow integration of various automated, semiautomated and/or manual biocuration pipelines, and provide researchers a user-friendly framework based on data mining, back-end data processing and biocuration
Results of previous one-on-one work with individual biologists and a small jamboree at 2017 International Gene Ontology Consortium meeting suggested that successful training required a well-defined project, multiple training sessions spread over several days, and a gradual introduction of tasks associated with the curation process to lead participants from familiar chores such as literature review to more specialized aspects of data organization and entry

Summary

Introduction

Big data generation in biology is becoming easier, cheaper and faster. scientists need cyber-infrastructure and platforms capable of providing a systems-level framework (genomic context) for visualization and analysis of highthroughput omics data in order to unleash the full potential of the data—which in turn can provide useful insights for translational research (see Figure 1). We summarize a successful biocuration jamboree (design, process, workflow and outcomes) and discuss strategies for enhancing the participation of the plant research community in biocuration of genes, proteins and pathways. Results of previous one-on-one work with individual biologists and a small jamboree at 2017 International Gene Ontology Consortium meeting suggested that successful training required a well-defined project, multiple training sessions spread over several days, and a gradual introduction of tasks associated with the curation process to lead participants from familiar chores such as literature review to more specialized aspects of data organization and entry. The participants mined genes from 7 published papers, provided detailed annotations for 200 genes and curated one complete regulatory pathway (HSFA7 gene network) and three partial pathways for the Plant Reactome database.

Data gathering on excel sheet

Visualization of a biological pathway and reactions

Drawing pathways and reactions using pathway curation tools

Conclusion