BRENDA in 2015: exciting developments in its 25th year of existence.
BRENDA in 2015: exciting developments in its 25th year of existence.
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DOI：
10.1093/nar/gku1068
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发表时间：
2015-01
影响因子：
14.9
通讯作者：
Schomburg D
中科院分区：
文献类型：
--
作者：
Chang A;Schomburg I;Placzek S;Jeske L;Ulbrich M;Xiao M;Sensen CW;Schomburg D
BRENDA酶信息系统（http：//www.brenda-enzymes.org/）已发展成为一个从不同来源获得的酶和酶配体信息的详细系统，并结合了灵活的查询系统和评价工具。这些信息是通过从主要文献、文本和数据挖掘、数据集成和预测算法中手动提取获得的。大约3亿个数据包括来自3万多个生物体的酶功能和分子数据。人工衍生的核心包含来自77000种酶的300万个数据，这些酶来自135000篇参考文献。每个条目都与参考文献和来源微生物相关联。它们由关于发生的信息、来自文本挖掘的酶/疾病关系、来自其他数据库的序列和3D结构以及预测的酶位置和基因组注释来补充。超过190，000种酶配体的功能和结构数据存储在BRENDA中。实施了改进功能和分析工具的新功能。人体解剖学图谱CAVEman与BRENDA组织本体论术语相关联，提供了解剖学和功能酶数据之间的联系。从PubMed摘要中获得的酶的Word Maps突出了酶的应用和科学相关性。改进了EnzymeDetector基因组注释工具和反应数据库BKM-react，包括来自BRENDA、KEGG和MetaCyc的反应。网站经过重新设计，提供了新的查询选项。
The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text and data mining, data integration, and prediction algorithms. Approximately 300 million data include enzyme function and molecular data from more than 30 000 organisms. The manually derived core contains 3 million data from 77 000 enzymes annotated from 135 000 literature references. Each entry is connected to the literature reference and the source organism. They are complemented by information on occurrence, enzyme/disease relationships from text mining, sequences and 3D structures from other databases, and predicted enzyme location and genome annotation. Functional and structural data of more than 190 000 enzyme ligands are stored in BRENDA. New features improving the functionality and analysis tools were implemented. The human anatomy atlas CAVEman is linked to the BRENDA Tissue Ontology terms providing a connection between anatomical and functional enzyme data. Word Maps for enzymes obtained from PubMed abstracts highlight application and scientific relevance of enzymes. The EnzymeDetector genome annotation tool and the reaction database BKM-react including reactions from BRENDA, KEGG and MetaCyc were improved. The website was redesigned providing new query options.
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影响因子：
14.9
作者：
Federhen S
通讯作者：
Federhen S
影响因子：
14.9
作者：
Chang A;Scheer M;Grote A;Schomburg I;Schomburg D
通讯作者：
Schomburg D
影响因子：
14.9
作者：
Gremse M;Chang A;Schomburg I;Grote A;Scheer M;Ebeling C;Schomburg D
通讯作者：
Schomburg D
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
14.9
作者：
Arnold R;Goldenberg F;Mewes HW;Rattei T
通讯作者：
Rattei T