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Sensing the cilium, digital capture of ciliary data for comparative genomics investigations

机译：传感纤毛，睫状数据的数字捕获，用于比较基因组学研究

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Cilia are specialized, hair-like structures that project from the cell bodies of eukaryotic cells. With increased understanding of the distribution and functions of various types of cilia, interest in these organelles is accelerating. To effectively use this great expansion in knowledge, this information must be made digitally accessible and available for large-scale analytical and computational investigation. Capture and integration of knowledge about cilia into existing knowledge bases, thus providing the ability to improve comparative genomic data analysis, is the objective of this work. We focused on the capture of information about cilia as studied in the laboratory mouse, a primary model of human biology. The workflow developed establishes a standard for capture of comparative functional data relevant to human biology. We established the 310 closest mouse orthologs of the 302 human genes defined in the SYSCILIA Gold Standard set of ciliary genes. For the mouse genes, we identified biomedical literature for curation and used Gene Ontology (GO) curation paradigms to provide functional annotations from these publications. Employing a methodology for comprehensive capture of experimental data about cilia genes in structured, digital form, we established a workflow for curation of experimental literature detailing molecular function and roles of cilia proteins starting with the mouse orthologs of the human SYSCILIA gene set. We worked closely with the GO Consortium ontology development editors and the SYSCILIA Consortium to improve the representation of ciliary biology within the GO. During the time frame of the ontology improvement project, we have fully curated 134 of these 310 mouse genes, resulting in an increase in the number of ciliary and other experimental annotations. We have improved the GO annotations available for mouse genes orthologous to the human genes in the SYSCILIA Consortium’s Gold Standard set. In addition, ciliary terminology in the GO itself was improved in collaboration with GO ontology developers and the SYSCILIA Consortium. These improvements to the GO terms for the functions and roles of ciliary proteins, along with the increase in annotations of the corresponding genes, enhance the representation of ciliary processes and localizations and improve access to these data during large-scale bioinformatic analyses.
机译：纤毛是从真核细胞的细胞体中突出的特殊的毛发状结构。随着对各种类型纤毛的分布和功能的了解的增加，对这些细胞器的兴趣正在增加。为了有效地利用这种知识的巨大扩展，必须以数字方式访问此信息，并将其用于大规模分析和计算研究。捕获和整合纤毛知识并将其整合到现有知识库中，从而提供改进比较基因组数据分析的能力，是这项工作的目标。我们专注于捕获关于纤毛的信息，这是在实验室小鼠（人类生物学的主要模型）中研究的。开发的工作流程建立了捕获与人类生物学相关的比较功能数据的标准。我们建立了SYSCILIA金标准睫状体基因组中定义的302个人类基因的310个最接近的小鼠直系同源基因。对于小鼠基因，我们确定了用于治愈的生物医学文献，并使用基因本体论（GO）治愈范例从这些出版物中提供功能性注释。我们采用一种以结构化，数字形式全面捕获纤毛基因实验数据的方法，从人类SYSCILIA基因组的小鼠直系同源基因开始，我们建立了一个工作流程，用于整理详细的纤毛蛋白分子功能和作用的实验文献。我们与GO Consortium本体开发编辑器和SYSCILIA Consortium紧密合作，以改善GO中睫状生物学的代表性。在本体改进项目的时间范围内，我们已经充分策划了这310个小鼠基因中的134个，从而导致纤毛和其他实验注释的数量增加。我们已经改进了SYSCILIA联盟金标准中与人类基因同源的小鼠基因可用的GO注释。此外，与GO本体开发人员和SYSCILIA联盟合作，改进了GO本身的睫状体术语。 GO术语对纤毛蛋白功能和作用的这些改进，以及相应基因注释的增加，增强了纤毛过程和定位的表示，并在大规模生物信息学分析中改善了对这些数据的访问。

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