From CVRG Wiki
Primary Data Management
We define "primary data" as data obtained directly from data acquisition instruments. While conversion tools may change the format of the file(s) the data are stored in, the underlying data are unchanged by the conversions. CVRG has developed six primary data management services. These are single nucleotide polymorphism (SNP), messenger RNA (mRNA) and protein expression, electrocardiography (ECG), imaging and clinical data services. Users can deploy whichever data services they need initially and others in the future, allowing for the expansion of primary data management as their project grows. Deployment can occur on servers managed by the CVRG at Johns Hopkins or managed by the users at their institutions. More details on deployment options can be found here.
OpenClinica is a free, open source clinical trial software platform for data management in clinical research. OpenClinica's design allows it to support all types of clinical studies in diverse research settings. The OpenClinica data service contains a portion of the OpenClinica 3.0 data model, focusing on subject, study and case report form information. More information on this service may be found here. The software itself can be found here.
The CVRG team has developed an open source, web-based software platform for the storage, visualization and annotation of diverse types of ECG time series data. These types include:
- HL7aECG - Health Level 7 annotated ECGs
- Norav - time series data produced by the Norav PC ECG 1200 software
- Physionet - Physionet WaveForm DataBase (WFDB) time series data
- GE MUSE - time series data exported by GE MUSE version 10 software
The CVRG team has deployed tools for managing DICOM image data. The RSNA Medical Imaging Resource Center (MIRC) project has constructed an image submission platform. Tools developed within MIRC provide clinical sites with software to securely forward DICOM images to Picture Archiving and Communication Systems (PACS) outside of their clinical site. The CVRG team is using these tools to transfer DICOM image files from scanners at study sites to the CVRG DICOM image data service.
dcm4chee is an open source PACS. The CVRG team is currently using dcm4chee as the management database for the DICOM image data service. More information on this service may be found here. The software itself can be found here.
The CVRG team is investigating the use of the Extensible Neuroimaging Archive Toolkit (XNAT), to manage DICOM files. XNAT is an open source software platform designed to facilitate management and exploration of imaging and related data. XNAT itself is already being used in the CVRG Imaging Analysis.
SNP Expression Data
The CVRG SNP data service is an open-source SNP data management system based upon the Cancer Genetic Markers of Susceptibility (CGEMS). The SNP data service supports the management of TaqMan, Illumina and Affymetrix data. More information on this service may be found here. The software itself can be found here.
mRNA Expression Data
caArray is an open-source mRNA array data management system developed as part of caBIG. caArray supports the annotation and exchange of mRNA array data. More information on this service may be found here. The software itself can be found here.
Proteomic Expression Data
ProteinDB is a full-featured proteomics data service based on the HUPO Proteomic Standards Initiative Object Model (PSI-OM). ProteinDB supports the management of gel electrophoresis, liquid chromatography, mass spectrometry and protein identification data. More information on this service may be found here. The software itself can be found here.
Data Analysis & Derived Data Management
CVRG has developed data analysis and derived data management services for ECG and imaging data. We define "derived data" to be data calculated from primary data.
ECG Analysis & Derived Data
The CVRG ECG Gadget is an open source software platform developed within the CVRG, using the Google Web Toolkit. A "Google gadget" is dynamic web content that can be placed on any web page. In our case, the gadgets are intended to be available through the CVRG Dashboard, based within iGoogle. The CVRG ECG Gadget supports ECG time series data submission and management, visualization, annotation, and analysis. Currently two data analsysis algorithms are deployed as services and are accessible from the ECG Gadget:
- The Berger Algorithm - developed by Dr. Ron Berger at Johns Hopkins University. See Berger, R.D., Kasper, E.K., Baughman K.L., Marban E., Calkins H., Tomaselli G.F. (1997) Beat-to-beat QT interval variability: novel evidence for repolarization lability in ischemic and nonischemic dilated cardiomyopathy. Circulation. 96(5):1557-1565 and Berger, R.D. (2003). QT Variability. J. Electrocardiol. 36: 83-87.
- The Physionet QT Algorithm - developed as part of the Physionet competition by Chesnokov et al.
Data may be passed into these algorithms, users may download all numeric results for import as an Excel spreadsheet, and results can be saved into an ECG derived data service. With input from the cardiovascular community, more algorithms can be added in the future.
The software for the ECG Gadget can be found here. More details on Berger data service may be found here and the Physionet QT data service can be found here. The software for the Berger data service can be found here and the Physionet QT data service can be found here.
Several tools for Cardiac Computational Anatomy have been integrated into an Imaging Analysis pipeline within the CVRG. These tools include:
- DicomBrowser - open source DICOM anonymization tool developed by the Neuroinformatics Research Group (NRG) at Washington University in St. Louis.
- K-PACS - free DICOM retrieval/viewing software developed by Dr. Andreas Knopke.
- Seg3D - segmentation tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute.
- Large Deformation Diffeomorphic Metric Mapping (LDDMM) - an application which aims to assign metric distances on the space of anatomical images in Computational Anatomy developed by the Center for Imaging Sciences at The Johns Hopkins University.
- 3DSlicer - a multi-platform, free open source software (FOSS) for visualization and image computing.
More information on these tools may be found here.
CVRG Cardiac Computational Anatomy results are maintained within XNAT. XNAT itself can be downloaded from here.
Decision Tree Algorithms & Analysis
The algorithms developed by the CVRG team are all written in the R programming language, building upon various existing R packages. The CVRG team also developed an open source, web-based software platform for the storage, analysis, visualization and retrieval of data sets by the algorithms. More information on the algorithms and the software platform may be found here. The software itself can be found here.
Primary & Derived Data Integration
CVRG iGoogle Federated Query Gadget
The CVRG iGoogle Federated Query Gadget is an open source software platform developed within the CVRG. It allows for complex querying across all the data within the CVRG Infrastructure (e.g., return all the multi-scale data for subjects born between 1930 and 1950 whose left ventricular ejection fraction is between 10 and 30 and whose TNF alpha receptor 2 measurement is greater than 3000). Users may visualize portions of the results within the Gadget and may download all the results for import as an Excel spreadsheet. More information on this platform may be found here. The software itself can be found here.