UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

被引：32

作者：

MacDougall, Alistair ^{[1
]}

Volynkin, Vladimir ^{[1
]}

Saidi, Rabie ^{[1
]}

Poggioli, Diego ^{[1
,2
]}

Zellner, Hermann ^{[1
]}

Hatton-Ellis, Emma ^{[1
]}

Joshi, Vishal ^{[1
]}

O'Donovan, Claire ^{[1
]}

Orchard, Sandra ^{[1
]}

Auchincloss, Andrea H. ^{[3
]}

Baratin, Delphine ^{[3
]}

Bolleman, Jerven ^{[3
]}

Coudert, Elisabeth ^{[3
]}

de Castro, Edouard ^{[3
]}

Hulo, Chantal ^{[3
]}

Masson, Patrick ^{[3
]}

Pedruzzi, Ivo ^{[3
]}

Rivoire, Catherine ^{[3
]}

Arighi, Cecilia ^{[4
]}

Wang, Qinghua ^{[4
]}

Chen, Chuming ^{[4
]}

Huang, Hongzhan ^{[4
]}

Garavelli, John ^{[4
]}

Vinayaka, C. R. ^{[5
]}

Yeh, Lai-Su ^{[5
]}

Natale, Darren A. ^{[5
]}

Laiho, Kati ^{[5
]}

Martin, Maria-Jesus ^{[1
]}

Renaux, Alexandre ^{[1
]}

Pichler, Klemens ^{[1
]}

机构：

[1] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England

[2] Kantar Consulting, I-40033 Bologna, Italy

[3] Ctr Med Univ Geneva, SIB Swiss Inst Bioinformat, CH-1211 Geneva 4, Switzerland

[4] Univ Delaware, Prot Informat Resource, Newark, DE 19711 USA

[5] Georgetown Univ, Prot Informat Resource, Med Ctr, Washington, DC 20007 USA

来源：

BIOINFORMATICS | 2020年 / 36卷 / 17期

基金：

美国国家卫生研究院; 英国生物技术与生命科学研究理事会; 美国国家科学基金会;

关键词：

D O I：

10.1093/bioinformatics/btaa485

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: 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. Results: 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.

引用

页码：4643 / 4648

页数：6

共 17 条

[1] UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase (vol 36, pg 4643, 2020)
MacDougall, Alistair
Volynkin, Vladimir
Saidi, Rabie
Poggioli, Diego
Zellner, Hermann
Hatton-Ellis, Emma
Joshi, Vishal
O'Donovan, Claire
Orchard, Sandra
Auchincloss, Andrea H.
Baratin, Delphine
Bolleman, Jerven
Coudert, Elisabeth
De Castro, Edouard
Hulo, Chantal
Masson, Patrick
Pedruzzi, Ivo
Rivoire, Catherine
Arighi, Cecilia
Wang, Qinghua
Chen, Chuming
Huang, Hongzhan
Garavelli, John
Vinayaka, C. R.
Yeh, Lai-Su
Natale, Darren A.
Laiho, Kati
Martin, Maria-Jesus
Renaux, Alexandre
Pichler, Klemens
BIOINFORMATICS, 2020, 36 (22-23) : 5562 - 5562
[2] Plant protein annotation in the UniProt knowledgebase
Schneider, M
Bairoch, A
Wu, CH
Apweiler, R
PLANT PHYSIOLOGY, 2005, 138 (01) : 59 - 66
[3] The UniProt Knowledgebase: a useful resource for developmental biology
Magrane, Michele
GENETICS RESEARCH, 2007, 89 (03) : 184 - 185
[4] SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase
David, Fabrice P. A.
Yip, Yum L.
BMC BIOINFORMATICS, 2008, 9 (1)
[5] SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase
Fabrice PA David
Yum L Yip
BMC Bioinformatics, 9
[6] UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase)
Soudy, Mohamed
Anwar, Ali Mostafa
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Ezzeldin, Shahd
Mahgoub, Sebaey
Magdeldin, Sameh
JOURNAL OF PROTEOMICS, 2020, 213
[7] UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB
Dogan, Tunca
MacDougall, Alistair
Saidi, Rabie
Poggioli, Diego
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O'Donovan, Claire
Martin, Maria J.
BIOINFORMATICS, 2016, 32 (15) : 2264 - 2271
[8] A Rule-Based Approach for Automatic Interaction Detection and Annotation
Sharaf, Nada
Abdennadher, Slim
Fruhwirth, Thom
2017 21ST INTERNATIONAL CONFERENCE INFORMATION VISUALISATION (IV), 2017, : 194 - 198
[9] Automatic rule learning for resource-limited MT
Carbonell, J
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MACHINE TRANSLATION: FROM RESEARCH TO REAL USERS, 2002, 2499 : 1 - 10
[10] The automatic annotation algorithm design and system implementation Rule-base function word usage
Yuan, Yingcheng
Zan, Hongying
Zhang, Kunli
Zhou, Yihui
11TH CHINESE LEXICAL SEMANTICS WORKSHOP (CKSW2010), 2010, : 165 - 171

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