Expert curation of plant proteins in UniProtKB/Swiss-Prot

The UniProtKB/Swiss-Prot Plant Protein Annotation Program has been actively collaborating with other resources. We recently started to collaborate with Araport, the Arabidopsis portal, and we provide Araport with all the gene model corrections that we introduced on the bases of our trans-species family annotation. We are also completing the knowledgebase by importing missing information from EnsemblPlants. Manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation of UniProtKB/TrEMBL entries to build comprehensive, high quality sets of proteins covering complete proteome of several plant species. The complete proteomes of Arabidopsis and rice are synchronized with the ones proposed by Araport and Gramene respectively. Data from high-throughput proteomics experiments constitute a rich potential source of annotations for UniProtKB. Certified experimental peptides that uniquely match the product of a single gene are used to generate annotations describing post-translational modifications and protein processing events, and to confirm protein existence. Around 2’600 Arabidopsis entries are now containing annotations extracted from 11 reviewed articles describing large scale proteomics experiments.