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- MetaCrop: a detailed database of crop plant metabolism

MetaCrop contains comprehensive, original, high-quality dataabout crop plant metabolism. While most of the existing metabolicpathway databases do not contain any plant-specific information,there exist a few multi-organism databases such as MetaCyc (19),BRENDA (21) and KEGG (16) comprising information about plantmetabolism. The transcriptome-based database EGENES (17) isa multi-species plant database, which currently consists of25 plant species (release 41.0, January 2007). The databaseintegrates plant genomic information (EST contigs) and pathwayinformation (pathway maps derived from KEGG reference pathways),thus offering an overview of fundamental biological processesin plants. In addition to these multi-species databases, thereexist a few species-specific crop plant databases such as thepathway/genome databases RiceCyc (http://www.gramene.org/pathway/)and SolCyc (http://www.sgn.cornell.edu/tools/solcyc/). However,most of these single- and multi-species databases only containlittle or no hand-curated information due to genome- or EST-basedpathway predictions or do not support model creation and modelexport in SBML. Furthermore, highly specific information suchas kinetic data, compartment-specific information or transportprocesses are often lacking and most of the databases are limitedto read-only access not allowing for user-specific interaction,editing and extending. Similar to MetaCrop the pathway databases AraCyc ((18), http://www.arabidopsis.org/biocyc/index.jsp)and MetNetDB ((27), http://www.metnetdb.org) contain detailedinformation about plant metabolism. AraCyc is a pathway/genomedatabase that contains enzymes and pathways found in the modelplant Arabidopsis (Arabidopsis thaliana). The Metabolic NetworkingData Base (MetNetDB) contains information on metabolic and regulatorynetworks in Arabidopsis, which are derived from a combinationof online databases and input from biologists in their areaof expertise. Both databases are under continued curation andcontain highly specific information such as compartment-specificinformation or transport processes. However, both databasescurrently only contain information about the model plant Arabidopsis.

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