Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.
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DOI：
10.1098/rsob.200149
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发表时间：
2020-09
期刊：
影响因子：
5.8
通讯作者：
Mungall CJ
中科院分区：
文献类型：
--
作者：
Wood V;Carbon S;Harris MA;Lock A;Engel SR;Hill DP;Van Auken K;Attrill H;Feuermann M;Gaudet P;Lovering RC;Poux S;Rutherford KM;Mungall CJ
生物过程是通过基因产物的协调作用来完成的。基因产物经常参与多个过程，因此可以被注释为多个基因本体论(GO)术语。然而，功能上、时间上和/或空间上相距较远的过程可能几乎没有共同的基因产物，而对不相关过程的共同注释可能反映了文献整理、本体结构或自动注释管道中的错误。我们已经开发了一种注释质量控制工作流程，它使用基于互斥过程的规则来检测注释错误，基于并通过案例研究进行验证，其中包括我们在这里提供的三个案例：随着时间的推移对裂解酵母蛋白编码基因的注释；人类和模式物种中粘连蛋白复合亚单位的注释；以及在人类和五个模式物种中使用一组选定的GO生物过程术语的注释。对于每个案例研究，我们审查了可用的GO注释，确定了不太可能被正确地共同注释到相同基因产物(例如氨基酸代谢和细胞质分裂)的生物过程对，并追踪了错误的注释的来源。到目前为止，我们已经生成了107条质量控制规则，并更正了289个真核生物的手动注释和超过52 700个跨所有分类群的自动传播注释。
Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.
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影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
DOI：
10.1093/database/bar068
发表时间：
2012
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Burge S;Kelly E;Lonsdale D;Mutowo-Muellenet P;McAnulla C;Mitchell A;Sangrador-Vegas A;Yong SY;Mulder N;Hunter S
通讯作者：
Hunter S
影响因子：
14.9
作者：
Mitchell A;Chang HY;Daugherty L;Fraser M;Hunter S;Lopez R;McAnulla C;McMenamin C;Nuka G;Pesseat S;Sangrador-Vegas A;Scheremetjew M;Rato C;Yong SY;Bateman A;Punta M;Attwood TK;Sigrist CJ;Redaschi N;Rivoire C;Xenarios I;Kahn D;Guyot D;Bork P;Letunic I;Gough J;Oates M;Haft D;Huang H;Natale DA;Wu CH;Orengo C;Sillitoe I;Mi H;Thomas PD;Finn RD
通讯作者：
Finn RD
影响因子：
4
作者：
Hodge, Christine A.;Choudhary, Vineet;Cole, Charles N.
通讯作者：
Cole, Charles N.
影响因子：
3.7
作者：
Alam-Faruque Y;Huntley RP;Khodiyar VK;Camon EB;Dimmer EC;Sawford T;Martin MJ;O'Donovan C;Talmud PJ;Scambler P;Apweiler R;Lovering RC
通讯作者：
Lovering RC