PPAP The UniProtKB/Swiss-Prot Plant Proteome Annotation Program

Basics on rice annotation

- Since the prediction of rice genes with unknown function still needs some improvement, we are currently concentrating our efforts on the annotation of characterized proteins and proteins families for which experimental data is available.

- Whenever possible, we are using the uniform gene nomenclature system (Os code) defined by RAP-DB and/or TIGR for the genome of Oryza sativa subspecies japonica, cultivar nipponbare.

- A list of all manually annotated rice proteins in UniProtKB/Swiss-Prot entries listed by gene number (Os code) can be found in the file rice.txt.

- The taxonomy classification used in UniProtKB/Swiss-Prot for Oryza sativa contains 3 different taxonomy identifiers: 39947 for japonica subspecies, 39946 for indica subspecies and 4530 for rice species (when subspecies are not specified). When available, cultivars are indicated in the "Reference Comment" lines of the entry.

- A list of the various rice cultivars cited in the "Reference Comment" lines of UniProtKB/Swiss-Prot entries, classified into the subspecies to which they belong (ORYSJ for japonica, ORYSI for indica, ORYSA when not specified), can be found in the file strains.txt.