Further development of the QuickGO web interface for browsing and retrieving Gene Ontology Annotation data

基因本体论（GO）联盟已经开发了一个本体论的描述基因和基因产物在一个标准化的格式。氧化石墨烯由三个结构化词汇组成，分别描述分子功能、生物过程和细胞成分。GO已成为基因产物注释的金标准，因为它可以方便地检索和比较来自同一或多个物种的基因产物。目前，在许多模式生物和基因组注释数据库中，约有20,000个GO术语用于描述基因产物。为了支持标准化的命名法，UniProt团队加入了GO注释工作，并启动了基因本体注释（GOA）项目，为蛋白质，特别是人类蛋白质组提供GO术语的分配。除了人工标注，GOA还提供超过10万个物种的自动计算机标注条目，并通过GO联盟成员和合作伙伴的标注补充GOA- uniprotkb数据。GOA是GO联盟注释工作中最大、最全面的开源注释贡献者。GO注释可以通过EBI或GO ftp站点下载，也可以从各种GO浏览器查询。然而，尽管有许多GO工具和浏览器可用，但没有一个可以执行GO用户经常要求的所有任务（GO Consortium Survey， 2005年10月）。缺乏干实验室经验的生物学家更喜欢查询简单的基于web的界面，但可能想要检索基因列表的GO注释并链接到其他数据库，而生物信息学家更喜欢以特定格式下载批量数据。但是，不可能通过现有接口进行批量检索，并且不同数据库的标识符之间的映射存在问题。QuickGO是第一个基于web的GO浏览器之一，非常有名并被广泛使用。QuickGO最初被设计为UniProtKB管理员的注释辅助工具，当其他人发现它也很有用时，它得到了进一步的发展。目前，它只允许用户搜索核心GO数据和单个UniProtKB添加、InterPro id或酶委员会（EC）编号的注释。随着用户请求数量的增加和对新功能的需求，需要进一步开发以满足用户群体不断增长的需求。此外，GOA-UniProtKB基因关联文件不断增加，变得笨拙，特别是对于只对注释子集感兴趣的用户。从该文件中检索特定数据变得非常繁琐，因此需要单个或批量检索GO和GOA数据的新方法。通过电子邮件和调查收集的用户需求表明，需要一种简单的基于web的工具来对带有任何标识符的GO注释执行批量查询，并查看和下载所有或一系列注释。因此，我们的目标是扩展QuickGO浏览器，以支持以下请求：-单个或批量搜索/提取GOA关联文件，FASTA或UniProtKB格式的数据，通过UniProtKB ID或登录号搜索单个或批量的基因或蛋白质- GO术语搜索/提取注释到GO术语的所有基因或蛋白质-单个或批量搜索替代ID，例如UniGene， DDBJ/EMBL/GenBank, Entrez, Ensembl, International Protein Index (IPI)， RefSeq等。GO本体和GOA数据通过引用的数量和web请求的规模以及ftp站点的数据下载证明了它们的受欢迎程度。GO的使用支持以标准化方式传播生物信息，我们应该提供必要的工具来支持和鼓励这些活动。通过扩展已经流行的QuickGO工具来促进更好的数据检索和操作，我们将使GO的追随者的庞大科学界受益，并为实验室科学家和生物信息学家提供有效的数据访问。

The Gene Ontology (GO) Consortium has developed an ontology for the description of genes and gene products in a standardised format. GO consists of three structured vocabularies to describe molecular function, biological process and cellular component. GO has become the gold standard for annotating gene products as it facilitates the efficient retrieval and comparison of gene products from the same or multiple species. Currently there are ~20,000 GO terms used to describe gene products in many model organism and genome annotation databases. In support of standardized nomenclature, the UniProt group joined the GO annotation effort and initiated the Gene Ontology Annotation (GOA) project to provide assignments of GO terms to proteins, particularly from the human proteome. In addition to manual annotation, GOA also provides automated in silico annotated entries for over 100,000 species, and supplements the GOA-UniProtKB data with annotations from the GO Consortium members and associates. GOA is the largest and most comprehensive open source contributor of annotations to the GO Consortium annotation effort. GO annotation can be downloaded via EBI or GO ftp sites or queried from various GO browsers. However, despite the fact that there are many GO tools and browsers available, none of these perform all the tasks frequently requested by GO Users (GO Consortium Survey, Oct 2005). Biologists with little dry lab experience prefer to query simple web-based interfaces, but may want to retrieve GO annotations for lists of genes and link to other databases, while Bioinformaticians prefer to download bulk data in specific formats. However, batch retrieval is not possible through existing interfaces, and problems exist with mapping between identifiers from different databases. QuickGO was one of the first web-based GO browsers and is well known and used extensively. QuickGO was initially designed as an annotation aid for UniProtKB curators, and developed further when others found it useful too. Currently, it simply enables users to search core GO data and annotations to single UniProtKB accessions, InterPro IDs or Enzyme Commission (EC) numbers. With the number of user requests increasing and new functionalities required, it needs to be developed further to keep up with the ever-increasing demands of the user community. In addition, the GOA-UniProtKB gene association file is constantly increasing and becoming unwieldy, especially for users only interested in a subset of annotations. Retrieving specific data from this file is becoming tedious, and new methods for single or bulk retrieval of GO and GOA data are essential. User requirements collected via e-mails and surveys indicate a need for a simple web-based tool to perform batch queries for GO annotation with any identifier, and to view and download ALL or sets of annotations. Our objectives are therefore to extend the QuickGO browser to enable the following requests: - Single or batch search /extraction of data in either GOA association file, FASTA or UniProtKB format for single or batches of genes or proteins searched by UniProtKB ID or accession number - GO term search /extraction of all genes or proteins annotated to a GO term - Single or batch searches for alternative IDs from e.g. UniGene, DDBJ/EMBL/GenBank, Entrez, Ensembl, International Protein Index (IPI), RefSeq, etc. The GO ontologies and GOA data have proven their popularity through the number citations and the scale of web requests and data downloads from ftp sites. The use of GO supports the communication of biological information in a standardised way, and we should be providing the tools necessary to support and encourage these activities. By extending the already popular QuickGO tool to facilitate better data retrieval and manipulation, we will benefit the enormous scientific community who are followers of GO, and provide efficient accessibility to the data for bench scientists and Bioinformaticians.