Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.
Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.
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DOI：
10.1093/database/bas045
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发表时间：
2012
期刊：
影响因子：
--
通讯作者：
Mouse Genome Informatics Database
中科院分区：
文献类型：
--
作者：
Drabkin HJ;Blake JA;Mouse Genome Informatics Database
小鼠基因组数据库、基因表达数据库和小鼠肿瘤生物学数据库是小鼠基因组信息学资源(http://www.informatics.jax.org).)的组成部分MGI系统既提供了关于实验室小鼠遗传学和基因组学知识的共识观点，也提供了实验观点。从基因到表型，这个信息资源整合了关于基因、序列、图谱、表达分析、等位基因、菌株和突变表型的信息。还提供了哺乳动物的比较数据，特别是关于使用小鼠作为研究人类疾病的分子和遗传成分的模型。这些数据来自文献整理以及大型数据集(SwissProt、LocusLink等)的下载。MGI是基因本体论(GO)的创始成员之一，并使用GO对基因进行功能注释。在这里，我们讨论与MGI的手动围棋注释相关的工作流程，从文献收集到注释的显示。同行评议的文献主要是从一套电子期刊中收集的。选定的文章被输入一个主书目，并被索引到八个感兴趣的领域中的一个，如“GO”、“Homology”或“表型”。然后，每篇文章要么被索引到数据库中已包含的基因，要么通过单独的命名数据库进行漏斗，以添加基因。主参考书目和相关的索引为各种馆长报告提供了信息，例如“被选为围棋的论文涉及没有围棋注释的基因”。一旦被编入索引，拥有适当学科专业知识的馆长就可以输入相关信息。MGI使用几个受控词汇表，以确保统一的数据编码、支持健壮的分析并支持复杂查询的构建。这些词汇从精选列表到围棋等结构化词汇都有。所有数据关联都有证据陈述和查阅来源出版物的支持。
The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as ‘GO’ or ‘homology’ or ‘phenotype’. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as ‘papers selected for GO that refer to genes with NO GO annotation’. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications.
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影响因子：
3
作者：
Van Auken K;Jaffery J;Chan J;Müller HM;Sternberg PW
通讯作者：
Sternberg PW
影响因子：
14.9
作者：
Finger JH;Smith CM;Hayamizu TF;McCright IJ;Eppig JT;Kadin JA;Richardson JE;Ringwald M
通讯作者：
Ringwald M
DOI：
10.1007/978-1-61779-361-5_11
发表时间：
2012-01-01
期刊：
BACTERIAL MOLECULAR NETWORKS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Latendresse, Mario;Paley, Suzanne;Karp, Peter D.
通讯作者：
Karp, Peter D.
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
影响因子：
9.5
作者：
Gaudet P;Livstone MS;Lewis SE;Thomas PD
通讯作者：
Thomas PD