Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.
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DOI：
10.1093/nar/gkw1075
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发表时间：
2017-01-04
影响因子：
14.9
通讯作者：
Wu CH
中科院分区：
文献类型：
--
作者：
Natale DA;Arighi CN;Blake JA;Bona J;Chen C;Chen SC;Christie KR;Cowart J;D'Eustachio P;Diehl AD;Drabkin HJ;Duncan WD;Huang H;Ren J;Ross K;Ruttenberg A;Shamovsky V;Smith B;Wang Q;Zhang J;El-Sayed A;Wu CH
蛋白质本体论（PRO; http：//purl.obolibrary.org/obo/pr）在三个主要领域正式定义和描述了分类特异性和分类中性蛋白质相关实体：进化相关的蛋白质;由给定基因产生的蛋白质;和含蛋白质的复合物。因此，PRO可以作为参考任何特异性水平的蛋白质实体的工具。为了增强这种能力，并促进不同资源中描述的此类实体的比较，我们使用UniProtKB作为序列参考和PSI-MOD作为翻译后修饰参考开发了蛋白质型的标准化表示。我们说明了它在促进PRO和Reactome蛋白实体之间的比对中的用途。我们还解决了可扩展性问题，描述了我们使用文本挖掘来识别蛋白质相关实体的第一步，从专家策划的资源中大规模导入蛋白质信息，以及我们动态生成PRO术语的能力。单个术语的Web视图现在可以提供更多关于密切相关术语的信息，包括例如交互式多序列比对。最后，我们描述了最近的改进语义效用，PRO现在表示在OWL和SPARQL端点。这些发展将进一步支持PRO的预期增长，并促进与蛋白质实体相关的数据的可重复性和聚合。
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities.
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影响因子：
64.8
作者：
Tran, John C.;Zamdborg, Leonid;Ahlf, Dorothy R.;Lee, Ji Eun;Catherman, Adam D.;Durbin, Kenneth R.;Tipton, Jeremiah D.;Vellaichamy, Adaikkalam;Kellie, John F.;Li, Mingxi;Wu, Cong;Sweet, Steve M. M.;Early, Bryan P.;Siuti, Nertila;LeDuc, Richard D.;Compton, Philip D.;Thomas, Paul M.;Kelleher, Neil L.
通讯作者：
Kelleher, Neil L.
影响因子：
14.9
作者：
Mi H;Poudel S;Muruganujan A;Casagrande JT;Thomas PD
通讯作者：
Thomas PD
影响因子：
14.9
作者：
Khare SP;Habib F;Sharma R;Gadewal N;Gupta S;Galande S
通讯作者：
Galande S
影响因子：
14.9
作者：
Natale DA;Arighi CN;Barker WC;Blake JA;Bult CJ;Caudy M;Drabkin HJ;D'Eustachio P;Evsikov AV;Huang H;Nchoutmboube J;Roberts NV;Smith B;Zhang J;Wu CH
通讯作者：
Wu CH
DOI：
10.1093/database/bav020
发表时间：
2015-03-31
影响因子：
5.8
作者：
Tudor, Catalina O.;Ross, Karen E.;Arighi, Cecilia N.
通讯作者：
Arighi, Cecilia N.