Overview

The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. This information is based on input from biologists in their area of expertise. In addition to the MetNet-curated interactions, we provide Aracyc-curated pathways and AGRIS-curated regulatory network. The data in MetNetDB is updated regularly.

Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another. Other fields describing the interactions are subcellular location, confidence, directionality, references, evidence, and synonyms. Data on entities (DNA, RNA, polypeptides, protein complexes, metabolites) are derived from web databases (gene related databases: TAIR, GO, MapMan/GabiPD; protein related databases: PPDB, AMPDB, AtNoPDB, AraPerox, PLprot, BRENDA; metabolite related databases: ChEBI, PubChem, KEGG, NCI compound library, NIST MS library), in some cases with additional annotation by experts.

Network information from MetNetDB can be converted to an XML file by XML Builder. From this XML file, it can be transferred to exploRase, which uses the network in conjunction with statistical analysis of expression data; to Cytoscape/FCM, which finds cycles and pathways in the network, and visualizes and models it in combination with expression data; and to MetNetVR, where the network can be visualized in 3D. XML Builder automatically builds new network XML files from the most current data in MetNetDB. A HiveMind-based service is also under extensive development to provide data in MetNetDB for all other MetNet tools under one integral platform.

For curators, we have provided a JAVA interface (Java 5.0 or later) to the MetNet database (see "Curator Tool").