COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies,Journal of Proteome Research

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COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2017-11-13 00:00:00 , DOI: 10.1021/acs.jproteome.7b00615
Dmitrii Travin ₁ , Iaroslav Popov ₁ , Arzu Tugce Guler ₂ , Dmitry Medvedev ₁ , Suzanne van der Plas-Duivesteijn ₂ , Monica Varela ₃ , Iris C. R. M. Kolder ₃ , Annemarie H. Meijer ₃ , Herman P. Spaink ₃ , Magnus Palmblad ₂

Affiliation

COMICS is an interactive and open-access web platform for integration and visualization of molecular expression data in anatomograms of zebrafish, carp, and mouse model systems. Anatomical ontologies are used to map omics data across experiments and between an experiment and a particular visualization in a data-dependent manner. COMICS is built on top of several existing resources. Zebrafish and mouse anatomical ontologies with their controlled vocabulary (CV) and defined hierarchy are used with the ontoCAT R package to aggregate data for comparison and visualization. Libraries from the QGIS geographical information system are used with the R packages “maps” and “maptools” to visualize and interact with molecular expression data in anatomical drawings of the model systems. COMICS allows users to upload their own data from omics experiments, using any gene or protein nomenclature they wish, as long as CV terms are used to define anatomical regions or developmental stages. Common nomenclatures such as the ZFIN gene names and UniProt accessions are provided additional support. COMICS can be used to generate publication-quality visualizations of gene and protein expression across experiments. Unlike previous tools that have used anatomical ontologies to interpret imaging data in several animal models, including zebrafish, COMICS is designed to take spatially resolved data generated by dissection or fractionation and display this data in visually clear anatomical representations rather than large data tables. COMICS is optimized for ease-of-use, with a minimalistic web interface and automatic selection of the appropriate visual representation depending on the input data.

中文翻译：

COMICS：使用解剖本体在空间语境中的Omics数据进行卡通可视化

COMICS是一个交互式且开放访问的Web平台，用于集成和可视化斑马鱼，鲤鱼和小鼠模型系统的解剖图中的分子表达数据。解剖本体用于以依赖于数据的方式在整个实验之间以及在实验和特定的可视化之间映射组学数据。COMICS建立在几种现有资源之上。带有受控词表（CV）和已定义层次结构的Zebrafish和鼠标解剖本体与onCAT R软件包一起使用，以汇总数据以进行比较和可视化。QGIS地理信息系统中的库与R包“ maps”和“ maptools”一起使用，以可视化模型系统的解剖图中的分子表达数据并与之交互。COMICS允许用户上传来自组学实验的自己的数据，只要使用CV术语来定义解剖区域或发育阶段，就可以使用他们希望的任何基因或蛋白质命名法。诸如ZFIN基因名称和UniProt保藏号之类的常见命名法提供了额外的支持。COMICS可用于在整个实验过程中生成基因和蛋白质表达的出版物质量的可视化图像。与以前的使用解剖本体论来解释包括斑马鱼在内的几种动物模型中的成像数据的工具不同，COMICS旨在获取解剖或分割产生的空间分辨数据，并以视觉上清晰的解剖学表示形式而不是大型数据表显示此数据。COMICS经过优化，易于使用，具有简约的Web界面，并根据输入数据自动选择适当的视觉表示。

更新日期：2017-11-14

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