Formalizing Phenotypes of Regeneration.
Formalizing Phenotypes of Regeneration.
复制标题
再生表型的形式化。
DOI：
10.1007/978-1-0716-2172-1_36
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Lobo,Daniel
中科院分区：
文献类型：
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作者：
Lobo,Daniel
再生实验可以产生复杂的表型，包括形态结果和基因表达模式，这对理解再生机制至关重要。然而，由于其固有的复杂性，个体之间的可变性，以及在文献中传播的异构数据，从中提取机械知识是当前的挑战。为了实现这一目标，我们提出了使用精确的数学形态学描述和标准化的基因表达模式来明确形式化再生表型及其实验程序的方案。我们说明了该方法的应用与一步一步的方案为涡虫和肢体再生表型。用这些方法整理的数据集不仅对人类科学家有帮助，而且它们代表了一个关键的形式化资源，可以很容易地集成到下游的逆向工程方法中，以自动提取机械知识。这种方法可以为发现全面的系统级再生模型铺平道路。
Regeneration experiments can produce complex phenotypes including morphological outcomes and gene expression patterns that are crucial for the understanding of the mechanisms of regeneration. However, due to their inherent complexity, variability between individuals, and heterogeneous data spreading across the literature, extracting mechanistic knowledge from them is a current challenge. Toward this goal, here we present protocols to unambiguously formalize the phenotypes of regeneration and their experimental procedures using precise mathematical morphological descriptions and standardized gene expression patterns. We illustrate the application of the methodology with step-by-step protocols for planaria and limb regeneration phenotypes. The curated datasets with these methods are not only helpful for human scientists, but they represent a key formalized resource that can be easily integrated into downstream reverse engineering methodologies for the automatic extraction of mechanistic knowledge. This approach can pave the way for discovering comprehensive systems-level models of regeneration.