Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase

Abstract

UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the 'Dicty annotation marathon', a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations.

Figure 1.

A modified gene model, commd10 (DDB_G0275249). (A) The gene prediction (underlined) selected a splice donor (gttaat) 21 nt upstream from that (gtaata) of the curated gene model (highlighted in yellow). This image was generated using the dictyBase Genome Browser. (B) The modified gene prediction is supported by sequence similarity. The new Dictyostelium gene model is indicated by a black shading of ‘DICTY’ on the labels on the left; the new gene model produces a better alignment than the gene prediction (bottom row), indicated by the gap in the alignment of the latter.

Figure 2.

The new dictyBase protein information page will display annotations from UniProtKB/Swiss-Prot. Information for the MhcA protein (gene ID: DDB_G0286355; sequence ID: DDB0191444) parsed from UniProtKB/Swiss-Prot record P08799 includes sequence processing, sequence existence evidence, subunit structure, post-translational modifications, as well as sub-cellular location. Fields obtained from UniProtKB/Swiss-Prot are marked with an asterisk.