Hammoud Zaynab, Kramer Frank
Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073 Göttingen, Germany.
Institute of Computer Science, IT Infrastructure for Translational Medical Research, University of Augsburg, Universitätsstraße 6a, 86159, Augsburg, Germany.
Genes (Basel). 2018 Oct 23;9(11):519. doi: 10.3390/genes9110519.
The modelling of complex biological networks such as pathways has been a necessity for scientists over the last decades. The study of these networks also imposes a need to investigate different aspects of nodes or edges within the networks, or other biomedical knowledge related to it. Our aim is to provide a generic modelling framework to integrate multiple pathway types and further knowledge sources influencing these networks. This framework is defined by a multi-layered model allowing automatic network transformations and documentation. By providing a tool that generates this model, we aim to facilitate the data integration, boost the reproducibility and increase the interoperability between different sources and databases in the field of pathways. We present R package that allows the user to create, modify and visualize graphs with multi-layers. The package is implemented with features to specifically handle multilayered graphs.
在过去几十年里，对诸如信号通路等复杂生物网络进行建模一直是科学家们的一项必要工作。对这些网络的研究也使得有必要研究网络中节点或边的不同方面，或与之相关的其他生物医学知识。我们的目标是提供一个通用的建模框架，以整合多种通路类型以及影响这些网络的进一步知识来源。这个框架由一个多层模型定义，允许自动进行网络转换和记录。通过提供一个生成此模型的工具，我们旨在促进数据整合，提高可重复性，并增强通路领域中不同来源和数据库之间的互操作性。我们展示了一个R包，它允许用户创建、修改和可视化多层图形。该包通过专门处理多层图形的功能来实现。
