MetaCyc and AraCyc. Metabolic pathway databases for plant research
MetaCyc and AraCyc. Metabolic pathway databases for plant research
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DOI：
10.1104/pp.105.060376
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发表时间：
2005-05-01
期刊：
影响因子：
7.4
通讯作者：
Rhee, SY
中科院分区：
文献类型：
--
作者：
Zhang, PF;Foerster, H;Rhee, SY
MetaCyc（http：//metacyc. org）包含实验确定的生化途径，用作代谢的参考数据库。与Pathway Tools软件结合使用，MetaCyc可用于计算预测注释基因组的代谢途径补充。为了增加途径和酶的广度，MetaCyc最近增加或更新了60多个植物特异性途径。与MetaCyc（其包含大范围生物体的代谢数据）相反，AraCyc是仅包含在模式植物拟南芥（Arabidopsis thaliana）中发现的酶和途径的物种特异性数据库。AraCyc（http：//arabidopsis. org/ tools/ aracyc/）是第一个来自MetaCyc的计算预测植物代谢数据库。自最初的计算构建以来，AraCyc一直在持续管理，以提高数据质量并增加途径覆盖的广度。最近从文献中人工筛选出了28条途径. AraCyc中的通路预测最近也更新了拟南芥基因的最新功能注释，这些注释使用了受控词汇和文献证据。AraCyc目前有1，418个独特的基因，映射到204个通路上，引用了1，156篇文献。Omics Viewer是一个用户数据可视化和分析工具，允许将具有实验值的基因、酶或代谢物列表绘制在AraCyc完整途径图的图表上。最近对MetaCyc和AraCyc的其他增强包括证据本体的实现，其已被用于提供关于数据质量的信息，途径本体的次级代谢节点的扩展以适应次级代谢途径的管理，以及用于存储和显示亚细胞区室内的酶和途径位置的细胞组分本体的增强。
MetaCyc ( http:// metacyc. org) contains experimentally determined biochemical pathways to be used as a reference database for metabolism. In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome. To increase the breadth of pathways and enzymes, more than 60 plant- specific pathways have been added or updated in MetaCyc recently. In contrast to MetaCyc, which contains metabolic data for a wide range of organisms, AraCyc is a species- specific database containing only enzymes and pathways found in the model plant Arabidopsis ( Arabidopsis thaliana). AraCyc ( http:// arabidopsis. org/ tools/ aracyc/) was the first computationally predicted plant metabolism database derived from MetaCyc. Since its initial computational build, AraCyc has been under continued curation to enhance data quality and to increase breadth of pathway coverage. Twenty- eight pathways have been manually curated from the literature recently. Pathway predictions in AraCyc have also been recently updated with the latest functional annotations of Arabidopsis genes that use controlled vocabulary and literature evidence. AraCyc currently features 1,418 unique genes mapped onto 204 pathways with 1,156 literature citations. The Omics Viewer, a user data visualization and analysis tool, allows a list of genes, enzymes, or metabolites with experimental values to be painted on a diagram of the full pathway map of AraCyc. Other recent enhancements to both MetaCyc and AraCyc include implementation of an evidence ontology, which has been used to provide information on data quality, expansion of the secondary metabolism node of the pathway ontology to accommodate curation of secondary metabolic pathways, and enhancement of the cellular component ontology for storing and displaying enzyme and pathway locations within subcellular compartments.