Rice Genes in Oryzabase

Abstract

In addition to maintaining a rice gene list, Oryzabase, a database of rice science, has also been hosting a website to submit newly identified genes. The current rice gene dictionary is based on a traditional rice trait gene dictionary and extended through time with new genes which are manually retrieved from journal articles. Currently over 4000 genes are listed. However it is still insufficient in both quantity and quality.Recently we started to apply automated extraction before manual annotation to enhance the efficiency of gene extraction. To improve the quality of information, we started collecting relevant DNA accessions and LOCUS-ID. In Oryzabase, we try to employ the help of users to overcome this information insufficiency by adding a comment box in each gene page to allow researchers to write additional information. Besides adding GO (gene ontology) and TO (trait ontology) to the genes, PO (plant ontology) has been newly assigned to enable better semantic query processing. The current status of gene extraction and ontology assignment and its related problems will be introduced.