MetaCrop is a manually curated repository of high quality information concerning the …

• Abstract
• Introduction
• Database description
• Curation, quality assurance, completeness and continuation
• Application of the metacrop database
• Discussion
• Conclusion
• Acknowledgment
• References
• Table 1
• Figure

All information was extracted manually through an extensivesurvey of primary literature and online databases. Literature-basedinformation was derived from about 800 papers of plant biochemicaland physiological journals as well as from respective textbooks(e.g. (14,15)). Furthermore, some of the information was manuallyextracted from online databases providing pathway-related information:KEGG PATHWAY ((16), http://www.genome.jp/kegg/pathway.html),EGENES ((17), http://www.genome.jp/kegg-bin/create_kegg_menu?category=plants_egenes),AraCyc ((18), http://www.arabidopsis.org/biocyc/index.jsp),MetaCyc ((19), http://metacyc.org/), RiceCyc (http://www.gramene.org/pathway/),Reactome ((20), http://www.reactome.org/); enzyme-related information:BRENDA ((21), http://www.brenda-enzymes.info/), ExPASy-ENZYME((22), http://expasy.org/enzyme/); protein-related information:Swiss-Prot/TrEMBL ((23), http://www.expasy.org/sprot/); metabolite-relatedinformation: PubChem (http://pubchem.ncbi), KEGG LIGAND ((16a),http://www.genome.jp/kegg/ligand.html); transporter-relatedinformation: ARAMEMNON ((24), http://aramemnon.botanik.uni-koeln.de/);kinetic information: BRENDA ((21), http://www.brenda-enzymes.info/)). For quality assurance information inferred from databases hasbeen checked against literature. To enable the trace back ofinformation and further reading, references and correspondingPubMed IDs are given where available. Controlled vocabulary(e.g. ontology terms from Plant Ontology (8) and Gene Ontology(9)) was used to ensure consistency and to allow the comparisonof data from different sources. Currently MetaCrop containsmost of the pathways of central metabolism in higher plants(e.g. metabolism of carbohydrates, amino acids, lipids, energy,cofactors and nucleotides). With respect to crop plant metabolism,special emphasis is laid on pathways of seed and tuber metabolismsuch as the sucrose breakdown pathway. While our current focusis on updating pathways with incomplete information, we planto extend the information stored in MetaCrop to pathways ofplant secondary metabolism. The extension of MetaCrop is primarydone inhouse; however, registered users can edit entries andextend the content of MetaCrop and therefore may in the futurealso contribute to the extension of the database.