UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
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DOI：
10.1093/bioinformatics/btaa485
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发表时间：
2020-11-01
期刊：
影响因子：
--
通讯作者：
UniProt Consortium
中科院分区：
文献类型：
--
作者：
MacDougall A;Volynkin V;Saidi R;Poggioli D;Zellner H;Hatton-Ellis E;Joshi V;O'Donovan C;Orchard S;Auchincloss AH;Baratin D;Bolleman J;Coudert E;de Castro E;Hulo C;Masson P;Pedruzzi I;Rivoire C;Arighi C;Wang Q;Chen C;Huang H;Garavelli J;Vinayaka CR;Yeh LS;Natale DA;Laiho K;Martin MJ;Renaux A;Pichler K;UniProt Consortium
由于基因组测序和蛋白质编码基因的预测，UniProt知识库（UniProtKB：https://www.uniprot.org）中的蛋白质记录的数量持续快速增长。为这些蛋白质提供功能注释是一个重大而持续的挑战。为了应对这一挑战，UniProt开发了一种基于专业策划规则的注释方法，称为UniRule，该方法集成了UniProt联盟成员开发的相关系统（RuleBase，HAMAP，PIRSR，PIRNR）。UniRule使用来自InterPro的蛋白质家族特征，结合分类学和其他约束，选择具有实验证据支持的共同功能特性的已审查蛋白质组。此注释被传播到UniProtKB中满足相同选择标准的未审查记录，其中大多数没有（也不可能有）经过实验验证的功能注释。UniProtKB的2020_01版本包含6496条UniRule规则，为5300万个蛋白质提供注释，占UniProtKB中1.78亿条记录的30%。UniRule在UniProtKB中提供可扩展的注释丰富。UniRule规则集成到UniProtKB中，可以在https://www.uniprot.org/unirule/上查看。UniRule规则和运行规则所需的代码，可供希望注释自己的序列的研究人员公开使用。用于运行规则的实现称为UniFIRE，可从https://gitlab.ebi.ac.uk/uniprot-public/unifire获得。
The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.
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影响因子：
14.9
作者：
Mitchell AL;Attwood TK;Babbitt PC;Blum M;Bork P;Bridge A;Brown SD;Chang HY;El-Gebali S;Fraser MI;Gough J;Haft DR;Huang H;Letunic I;Lopez R;Luciani A;Madeira F;Marchler-Bauer A;Mi H;Natale DA;Necci M;Nuka G;Orengo C;Pandurangan AP;Paysan-Lafosse T;Pesseat S;Potter SC;Qureshi MA;Rawlings ND;Redaschi N;Richardson LJ;Rivoire C;Salazar GA;Sangrador-Vegas A;Sigrist CJA;Sillitoe I;Sutton GG;Thanki N;Thomas PD;Tosatto SCE;Yong SY;Finn RD
通讯作者：
Finn RD
影响因子：
12.3
作者：
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通讯作者：
Maglott, Donna R.
DOI：
10.1093/database/baz026
发表时间：
2019-02-26
影响因子：
5.8
作者：
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通讯作者：
Wu, Cathy H.
影响因子：
14.9
作者：
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通讯作者：
Chibucos MC
DOI：
10.1093/bioinformatics/btu031
发表时间：
2014-05-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Jones P;Binns D;Chang HY;Fraser M;Li W;McAnulla C;McWilliam H;Maslen J;Mitchell A;Nuka G;Pesseat S;Quinn AF;Sangrador-Vegas A;Scheremetjew M;Yong SY;Lopez R;Hunter S
通讯作者：
Hunter S