iplants: A Repository of Plant Metabolic Data
摘要
Studying plant metabolism is crucial for understanding plant development and acclimation. However, plant metabolism is highly complex and knowledge of plant enzymes and metabolic pathways is still limited, which hampers the understanding of plant behaviour. The existence of a centralised repository to organise relevant plant data is of utmost importance for facilitating the study of plant metabolism. Here, a repository named iplants was created to integrate metabolic data from PlantCyc and MetaCyc databases, enzyme data from UniProt, and the content of plant genome-scale metabolic models. iplants includes tools to extract, transform, and integrate data from different sources into the centralised repository, a pipeline for the automatic update of the repository data, and an application programming interface to allow automatic access to the data. In total, iplants includes 24,333 metabolites, 205,128 reactions, 3,519 pathways, and 22,433 enzymes, 72% of which have a protein sequence. Plant enzymes represent only 21% of the enzymes in the database, which reflects the poor annotation of plant genomes.