MOTIVATION Morphological and genetic spatial data from functional experiments based on genetic, surgical and pharmacological perturbations are being produced at an extraordinary pace in developmental and regenerative biology. However, our ability to extract knowledge from these large datasets are hindered due to the lack of formalization methods and tools able to unambiguously describe, centralize and interpret them. Formalizing spatial phenotypes and gene expression patterns is especially challenging in organisms with highly variable morphologies such as planarian worms, which due to their extraordinary regenerative capability can experimentally result in phenotypes with almost any combination of body regions or parts. RESULTS Here, we present a computational methodology and mathematical formalism to encode and curate the morphological outcomes and gene expression patterns in planaria. Worm morphologies are encoded with mathematical graphs based on anatomical ontology terms to automatically generate reference morphologies. Gene expression patterns are registered to these standard reference morphologies, which can then be annotated automatically with anatomical ontology terms by analyzing the spatial expression patterns and their textual descriptions. This methodology enables the curation and annotation of complex experimental morphologies together with their gene expression patterns in a centralized standardized dataset, paving the way for the extraction of knowledge and reverse-engineering of the much sought-after mechanistic models in planaria and other regenerative organisms. AVAILABILITY AND IMPLEMENTATION We implemented this methodology in a user-friendly graphical software tool, PlanGexQ, freely available together with the data in the manuscript at https://lobolab.umbc.edu/plangexq. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

中文翻译：

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带有分段参考形态的涡虫基因表达模式的管理和注释。

动机在发育和再生生物学中，以遗传，外科和药理扰动为基础的功能性实验的形态学和遗传空间数据正以惊人的速度产生。但是，由于缺乏能够明确描述，集中和解释它们的形式化方法和工具，我们从这些大型数据集中提取知识的能力受到了阻碍。在具有高度可变形态的生物（例如planar虫）中，使空间表型和基因表达模式形式化尤其具有挑战性，由于其非凡的再生能力，它们在实验上会产生几乎任何身体部位或部位组合的表型。结果在这里，我们提出了一种计算方法和数学形式主义，以编码和管理平面虫的形态学结果和基因表达模式。蠕虫形态是根据解剖本体术语用数学图进行编码的，以自动生成参考形态。基因表达模式已注册到这些标准参考形态，然后可以通过分析空间表达模式及其文本描述，自动使用解剖本体术语进行注释。这种方法可以在中央标准化数据集中管理和注释复杂的实验形态及其基因表达模式，为在平面虫和其他再生生物中广受欢迎的力学模型的知识提取和逆向工程铺平了道路。可用性和实现我们在用户友好的图形软件工具PlanGexQ中实现了该方法，该工具可与https://lobolab.umbc.edu/plangexq上​​的手稿中的数据免费提供。补充信息补充数据可从Bioinformatics在线获得。