Planform: an application and database of graph-encoded planarian regenerative experiments.
Planform: an application and database of graph-encoded planarian regenerative experiments.
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Planform：图形编码涡虫再生实验的应用程序和数据库。
DOI：
10.1093/bioinformatics/btt088
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发表时间：
2013
期刊：
影响因子：
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通讯作者：
Levin,Michael
中科院分区：
文献类型：
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作者：
Lobo,Daniel;Malone,TaylorJ;Levin,Michael
了解许多生物体再生能力的机制是生物学和医学的一个基本兴趣。越来越多的操作和分子实验正试图发现一个全面的再生模型，其中Planarian扁形虫是最重要的模式物种之一。尽管付出了很多努力，但还没有全面的，建设性的，机械的模型存在，现在很明显，需要计算工具来挖掘这个巨大的数据集。然而，到目前为止，还没有再生实验的数据库，并且当前的基因型-表型本体和数据库是基于文本描述的，这是计算机无法理解的。为了克服这些困难，我们在这里提出Planform（Planarian formalization），一个手动策划的数据库和软件工具的Planarian再生实验，基于数学图形形式主义。该数据库包含了来自主要出版物的一千多个实验。该软件工具为用户提供了一个图形界面，可以轻松地与数据库进行交互和挖掘。该系统是再生社区的宝贵资源，更重要的是，将为应用新的人工智能工具从该数据集中提取知识铺平道路。可用性：数据库和软件工具可在www.example.com免费获得：michael. tufts.edu http://planform.daniel-lobo.com.Contact
Summary:Understanding the mechanisms governing the regeneration capabilities of many organisms is a fundamental interest in biology and medicine. An ever-increasing number of manipulation and molecular experiments are attempting to discover a comprehensive model for regeneration, with the planarian flatworm being one of the most important model species. Despite much effort, no comprehensive, constructive, mechanistic models exist yet, and it is now clear that computational tools are needed to mine this huge dataset. However, until now, there is no database of regenerative experiments, and the current genotype–phenotype ontologies and databases are based on textual descriptions, which are not understandable by computers. To overcome these difficulties, we present here Planform (Planarian formalization), a manually curated database and software tool for planarian regenerative experiments, based on a mathematical graph formalism. The database contains more than a thousand experiments from the main publications in the planarian literature. The software tool provides the user with a graphical interface to easily interact with and mine the database. The presented system is a valuable resource for the regeneration community and, more importantly, will pave the way for the application of novel artificial intelligence tools to extract knowledge from this dataset.Availability:The database and software tool are freely available at http://planform.daniel-lobo.com.Contact:michael.levin@tufts.edu