Ontology of Arabidopsis gene net supplementary database (AGNS), cross database references to tair ontology

Motivation: Inter-database queries on the same subject domain require a coordinated vocabulary of terms. The existing plant ontology (PO) has been made mainly for description of large-scale experiments and contains gaps, which should be filled to provide terms for description of gene expression patterns revealed by in situ hybridization and phenotype abnormalities in mutant and transgenic plants. Results: We have created an Arabidopsis PO based on controlled vocabularies of AGNS (Arabidopsis Gene Net Supplementary) database, which contains a detailed information on anatomical elements and development stages from annotated papers on gene expression and phenotype abnormalities in mutant and transgenic plants. The comparison of ANGS ontology with PO allowed us to develop a common ontology providing both inter-database queries based on general standards and an opportunity to describe the whole scale of transcriptomic and phenomic data in the course of Arabidopsis development.