GeneToList: A Web Application to Assist with Gene Identifiers for the Non-Bioinformatics-Savvy Scientist.
GeneToList: A Web Application to Assist with Gene Identifiers for the Non-Bioinformatics-Savvy Scientist.
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随着组学技术的日益普及，许多科学家第一次处理大量的基因组数据。虽然有许多惊人的生物信息学工具可用于帮助分析这些数据，但这些科学家面临的一个共同困难是，并非所有基因数据或分析工具都使用相同的基因组命名法。另一个问题是，许多出版物仍然使用过时的或口语化的基因别名，而不是官方的基因标识符。常见的基因ID转换工具和其他下游分析软件与这些基因别名作斗争。因此，我们开发了一个免费和公开的Web应用程序，GeneToList，以协助基因ID消歧和基因ID转换，特别关注非生物信息学精通科学家的用户友好界面。组学技术越来越多地融入生物医学研究和转化医学，这给这些方法生成的大型复杂数据集的最终用户带来了挑战。基因组学中的一个特殊挑战是，大型基因组数据库之间或常用的遗传分析工具之间的基因命名并不统一。此外，过时的基因组命名法仍然可以在科学交流中找到，包括同行评审的手稿。因此，开发了一个网络应用程序（GeneToList），以帮助基因ID转换和别名匹配，特别关注为非生物信息学精通的科学家实现用户友好的界面。它目前包括从国家生物技术和信息中心（NCBI）基因资源检索的38，000多个不同分类群的基因信息。支持的基因ID数据库包括NCBI Gene Symbols、NCBI Gene ID（NCBI Gene ID）、OMIM ID、HGNC ID、Ensembl ID和28个其他分类群特异性标识符。GeneToList可在genetolist.com上获得。该工具是一个与许多标准浏览器兼容的Web应用程序。发现该应用程序的基因ID转换功能优于常见的基因ID转换工具。具体来说，它能够成功转换所有测试ID，而其他人则无法识别基因别名。因此，当基因命名的一致性对下游分析很重要时，该应用程序提供的基因ID消歧应该对处理基因数据的许多科学家有益。
With the increasing popularity of omics technologies, many scientists are dealing with large sets of genomic data for the first time. While there are many amazing bioinformatics tools available to help analyze this data, one common difficulty these scientists face is that not all gene data or analysis tools use the same genomic nomenclature. Another issue is that many publications still use obsolete or colloquial gene aliases instead of official gene identifiers. Common gene ID conversion tools and other downstream analysis software struggle with these gene aliases. Therefore, we developed a free and publicly available web application, GeneToList, to assist in gene ID disambiguation and gene ID conversion, with a specific focus on a user-friendly interface for the non-bioinformatics-savvy scientist. The increasing incorporation of omics technologies into biomedical research and translational medicine presents challenges to end users of the large and complex datasets that are generated by these methods. A particular challenge in genomics is that the nomenclature for genes is not uniform between large genomic databases or between commonly used genetic analysis tools. Furthermore, outdated genomic nomenclature can still be found amongst scientific communications, including peer-reviewed manuscripts. Therefore, a web application (GeneToList) was developed to assist in gene ID conversion and alias matching, with a specific focus on achieving a user-friendly interface for the non-bioinformatics-savvy scientist. It currently includes gene information for over 38,000 different taxa retrieved from the National Center for Biotechnology and Information (NCBI) Gene resource. Supported databases of gene IDs include NCBI Gene Symbols, NCBI Gene IDs (Entrez IDs), OMIM IDs, HGNC IDs, Ensembl IDs, and 28 other taxa-specific identifiers. GeneToList is available at genetolist.com. The tool is a web application that is compatible with many standard browsers. The gene ID conversion feature of this application was found to outcompete the common gene ID conversion tools. Specifically, it was able to successfully convert all tested IDs, whereas the others were not able to recognize the gene aliases. Therefore, the gene ID disambiguation provided by this application should be beneficial for many scientists dealing with gene data when the uniformity of gene nomenclature is important for downstream analysis.
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