Depicts and integrates the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. AtPID predicts the Protein-protein interaction pairs by integrating several methods with the Naive Baysian Classifier. All other related information curated in the AtPID is manually extracted from published literatures and other resources from some expert biologists. AtPID collects 5564 mutants with significant morphological alterations which were manually curated to 167 plant ontology (PO) morphology categories and predicts 4457 high confidence gene-PO pairs with 1369 genes as the complement. These single/multiple-gene mutants are indexed and linked to 3919 genes.