Developing the Apollo software for high-throughput annotation of multiple genomes

基因组测序变得越来越便宜和强大。然而， 利用这些数据的科学进步是高质量基因组的产生 注释，描述基因组DNA中基因的位置和功能。在 过去，这些注释完全由专业生物制造商生成， 这些生物浓缩器仍然是一个重要的专门知识来源。但是，数量 与可用的基因组DNA的量相比，这样的生物浓缩剂是小的。在 近年来，越来越多的志愿者补充了专业的生物护理 感兴趣的生物学家的力量，每个人通常对一两个感兴趣的基因感兴趣。 尽管基因组注释通常使用计算工具批量完成，但 目前没有替代手动注释的最后一遍。这是最常见 使用我们的Apollo软件完成，该软件允许实时同步协作 网络上的注释。我们的建议是改进阿波罗计划， 专业的生物制造者和众包志愿者。我们将赋予专业人士 通过给他们所需的电动工具， 多个基因组（通过利用共线性），注释变体，并注释功能 基因。我们将通过降低准入门槛， 让阿波罗更有用对于所有用户，我们将训练机器学习系统， 自动检测常见的注释错误并提出改进建议。我们将 支持Apollo用户的维护、错误修复和各种功能请求，以及 包括开发商在内的广泛推广。

Genome sequencing is becoming cheaper and more powerful. However, a bottleneck to scientific progress using these data is the generation of high-quality genome annotations, describing the location and function of the genes in genomic DNA. In the past, these annotations were generated exclusively by professional biocurators, and these biocurators continue to be a critical source of expertise. However, the number of such biocurators is small compared to the amount of genomic DNA that is available. In recent years, professional biocuration has been supplemented by a growing volunteer force of interested biologists, each generally interested in one or two genes of interest. Although genome annotation is often done in bulk using computational tools, there is currently no substitute for a final pass of manual annotation. This is most commonly done using our Apollo software, which allows for live simultaneous collaborative annotation over the web. Our proposal here is to improve Apollo so as to empower both professional biocurators and crowdsourcing volunteers. We will empower professional biocurators by giving them the power tools they need to simultaneously annotate multiple genomes (by exploiting synteny), annotate variants, and annotate the function of genes. We will empower the crowdsourcing volunteers by lowering barriers to entry, making Apollo more usable. For all users we will train machine learning systems to automatically detect common annotation errors and suggest improvements. We will support Apollo users with maintenance, bugfixing, and various feature requests, as well as extensive outreach including outreach to developers.