He Sijin, Yong May, Matthews Paul M, Guo Yike
European Bioinformatics Institute, Cambridge, UK.
Data Science Institute, Imperial College London, London, UK.
Bioinformatics. 2017 Mar 1;33(5):787-788. doi: 10.1093/bioinformatics/btw714.
TranSMART has a wide range of functionalities for translational research and a large user community, but it does not support imaging data. In this context, imaging data typically includes 2D or 3D sets of magnitude data and metadata information. Imaging data may summarise complex feature descriptions in a less biased fashion than user defined plain texts and numeric numbers. Imaging data also is contextualised by other data sets and may be analysed jointly with other data that can explain features or their variation.
Here we describe the tranSMART-XNAT Connector we have developed. This connector consists of components for data capture, organisation and analysis. Data capture is responsible for imaging capture either from PACS system or directly from an MRI scanner, or from raw data files. Data are organised in a similar fashion as tranSMART and are stored in a format that allows direct analysis within tranSMART. The connector enables selection and download of DICOM images and associated resources using subjects' clinical phenotypic and genotypic criteria.
tranSMART-XNAT connector is written in Java/Groovy/Grails. It is maintained and available for download at https://github.com/sh107/transmart-xnat-connector.git.
TranSMART具有一系列用于转化研究的功能以及庞大的用户群体，但它不支持成像数据。在此背景下，成像数据通常包括二维或三维的幅度数据集以及元数据信息。与用户定义的纯文本和数字相比，成像数据可以以较少偏差的方式总结复杂的特征描述。成像数据还可以通过其他数据集进行情境化处理，并可以与能够解释特征或其变化的其他数据联合分析。
在此，我们描述了我们开发的tranSMART-XNAT连接器。该连接器由用于数据捕获、组织和分析的组件组成。数据捕获负责从PACS系统或直接从MRI扫描仪或从原始数据文件中进行成像捕获。数据以与TranSMART类似的方式进行组织，并以允许在TranSMART内直接分析的格式存储。该连接器能够使用受试者的临床表型和基因型标准选择和下载DICOM图像及相关资源。
tranSMART-XNAT连接器用Java/Groovy/Grails编写。它在https://github.com/sh107/transmart-xnat-connector.git上维护并可供下载。
