DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more.
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more.
复制标题
DOI：
10.1093/nar/gks1080
复制
发表时间：
2013-01
影响因子：
14.9
通讯作者：
Gough J
中科院分区：
文献类型：
--
作者：
Fang H;Gough J
我们提出了'dcGO'（http：//supfam.org/SUPERFAMILY/dcGO），一个全面的蛋白质领域的本体数据库。结构域通常是蛋白质的功能单位，因此，与其将本体论术语仅与全长蛋白质相关联，有时将术语与单个结构域相关联更有意义。以结构域为中心的GO，'dcGO'，提供了本体论术语和蛋白质结构域之间在超家族和家族水平上的关联。一些功能单元由一个以上的结构域共同作用或在结构域之间的界面上作用组成;因此，还提供了与结构域对、三联体和更长的超结构域相关的本体论术语。在撰写本文时，dcGO中的本体包括基因本体（GO）;酶委员会（EC）编号;来自UniPathway的途径;人类表型本体和来自五种模式生物（包括植物）的表型本体;来自三种生物的解剖学本体;来自DrugBank的人类疾病本体和药物。所有本体论术语都有其关联的概率得分。除了与结构域和超结构域的关联之外，本体论术语已经通过同源性转移到蛋白质，提供超过8000万个序列的注释，覆盖2414个完整的基因组，数百个元基因组，数千个病毒等。dcGO数据库每两周更新一次，其网站提供下载、搜索、浏览、系统发育背景和其他数据挖掘设施。
We present ‘dcGO’ (http://supfam.org/SUPERFAMILY/dcGO), a comprehensive ontology database for protein domains. Domains are often the functional units of proteins, thus instead of associating ontological terms only with full-length proteins, it sometimes makes more sense to associate terms with individual domains. Domain-centric GO, ‘dcGO’, provides associations between ontological terms and protein domains at the superfamily and family levels. Some functional units consist of more than one domain acting together or acting at an interface between domains; therefore, ontological terms associated with pairs of domains, triplets and longer supra-domains are also provided. At the time of writing the ontologies in dcGO include the Gene Ontology (GO); Enzyme Commission (EC) numbers; pathways from UniPathway; human phenotype ontology and phenotype ontologies from five model organisms, including plants; anatomy ontologies from three organisms; human disease ontology and drugs from DrugBank. All ontological terms have probabilistic scores for their associations. In addition to associations to domains and supra-domains, the ontological terms have been transferred to proteins, through homology, providing annotations of >80 million sequences covering 2414 complete genomes, hundreds of meta-genomes, thousands of viruses and so forth. The dcGO database is updated fortnightly, and its website provides downloads, search, browse, phylogenetic context and other data-mining facilities.
登录
查看更多内容
影响因子：
14.9
作者：
Grumbling G;Strelets V
通讯作者：
Strelets V
影响因子：
46.9
作者：
Smith, Barry;Ashburner, Michael;Lewis, Suzanna
通讯作者：
Lewis, Suzanna
影响因子：
14.9
作者：
de Lima Morais DA;Fang H;Rackham OJ;Wilson D;Pethica R;Chothia C;Gough J
通讯作者：
Gough J
影响因子：
12.3
作者：
Mungall CJ;Gkoutos GV;Smith CL;Haendel MA;Lewis SE;Ashburner M
通讯作者：
Ashburner M
影响因子：
14.9
作者：
Bradford Y;Conlin T;Dunn N;Fashena D;Frazer K;Howe DG;Knight J;Mani P;Martin R;Moxon SA;Paddock H;Pich C;Ramachandran S;Ruef BJ;Ruzicka L;Bauer Schaper H;Schaper K;Shao X;Singer A;Sprague J;Sprunger B;Van Slyke C;Westerfield M
通讯作者：
Westerfield M