Department of Biology, Center for Regenerative and Developmental Biology, Tufts University, 200 Boston Avenue, Medford, MA 02155, USA.
Bioinformatics. 2013 Apr 15;29(8):1098-100. doi: 10.1093/bioinformatics/btt088. Epub 2013 Feb 19.
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.
The database and software tool are freely available at http://planform.daniel-lobo.com.
了解许多生物体再生能力的调控机制是生物学和医学的一个基本关注点。越来越多的操作和分子实验试图发现一个全面的再生模型，而扁形动物涡虫是最重要的模式生物之一。尽管付出了巨大的努力，但目前仍然没有全面的、建设性的、机械性的模型存在，现在显然需要计算工具来挖掘这个巨大的数据集。然而，直到现在，还没有再生实验的数据库，目前的基因型-表型本体论和数据库都是基于文本描述的，计算机无法理解。为了克服这些困难，我们在这里提出了 Planform（扁形动物形式化），这是一个基于数学图形式主义的扁形动物再生实验的手动编目数据库和软件工具。该数据库包含了主要扁形动物文献中的一千多个实验。该软件工具为用户提供了一个图形界面，方便用户与数据库进行交互和挖掘。所提出的系统是再生社区的宝贵资源，更重要的是，它将为应用新型人工智能工具从这个数据集提取知识铺平道路。
数据库和软件工具可在 http://planform.daniel-lobo.com 免费获取。
