Web Services

As an NHLBI resource, the CVRG is committed to the delivery of tools, for sharing and analyzing cardiovascular data. Four different groups of tools are under development or have been deployed. These are: 1) an ECG storage and analysis interface; 2) a customized instance of XNAT for cardiovascular imaging & imaging analysis; 3) an optimized representation tool for clinical data; and 4) a workflow tool for data retrieval & analysis. Within these groups, data and analytical services are combined to meet the needs of the Driving Biomedical Projects. The tools are described in detail on the CVRG Wiki, and are listed below:

ECG services

ECGrid Toolkit

The ECGrid Toolkit is a web interface that allows upload, download, visualization/annotation, analysis and viewing of the analysis results. The web interface serves as the entry/access point to a number of underlying services that perform these functions. All these services make use of an XML database and file system. The file system stores the ECGs in an open-source format (WaveForm DataBase; WFDB) developed as part of the Physionet resource. The XML database stores metadata about the ECG files (e.g., where they are located, what the names of the files are, etc.) along with manual and automated annotation performed using the visualization/annotation and analysis services of the Toolkit.

ECG Analysis Services

QT Screening Algorithm

The QT Screening Algorithm is a web service that implements an automated QT detection algorithm developed as part of the Computers in Cardiology 2006 Challenge, by Yuriy Chesnokov, whose paper on the algorithm can be found here. The CVRG extended this tool to compute corrected QT and the QT Variability Index. The service itself accepts files in Physionet WaveForm Database WFDB and produces XML output containing the results.

QRS Score Algorithm

The QRS Score Algorithm is a web service that implements a Java implementation of the Strauss Selvester QRS score. Details on the algorithm itself can be found in Strauss DG, et. al. (2009) J Electrocardiol. 42(1):85-96;.The service produces a comma separated value file with all the computed scar values and the overall Strauss Selvester QRS score.

Imaging Services

XNAT-CVI

XNAT-CVI is an extension to the eXtensible NeuroImaging Archive Toolkit (XNAT), developed by Dan Marcus’ team at Washington University in St. Louis. Extensions within XNAT-CVI include the ability to store ultrasound (US) imaging, workflows to process US, computed tomography (CT) and magnetic resonance (MR) using cardiac imaging analysis tools and the association of the analysis results with the original imaging datasets.
Within XNAT exists the Pipeline Engine, a Java-based framework that links sequential activities, human and computer, into a defined process flow and manages how data moves from step to step in that flow based on the results of each step. Pipelines can be executed up to a step, then notify a user(s) to perform the manual task, and finally restart the pipeline from the next step. The process flow is defined in am XML document called the pipeline descriptor and the executables are defined in a separate XML document called resource descriptors.

LDDMM/DiffeoMap

LDDMM

LDDMM is an application which aims to assign metric distances on the space of anatomical images in Computational Anatomy developed by the Center for Imaging Science at The Johns Hopkins University. It has been applied to brain morphology. Its application within the CVRG deals with heart morphology, with respect to heart shape and motion.

DiffeoMap

DiffeoMap is a desktop client application that allows users to perform image registration/transformation and remotely process the registered images using LDDMM.

Clinical Services

CVRG Registry

Clinical data warehouses frequently are structured in a generalized way that supports many constituencies. For research, there is a need to transform these heterogeneous data into a shared representation, and to perform categorization and interpretation to optimize the data representation for investigators. We are addressing this need by extending an existing clinical database query system, PROTEMPA that can execute temporal queries and extract longitudinal summaries of patient data. The extended system allows specifying data types of interest in federated databases, extracting the data into a shared representation, transforming it through categorization and interpretation, and loading it into a registry database that can be refreshed. Such a registry’s access control, data representation and query tools can be tailored to the needs of research while keeping local databases as the source of truth. The Analytic Information Warehouse is an extension to i2b2 that integrates a Protégé Web Server as the common data element/ontology mapping repository. Its intent is to be able to integrate data from multiple clinical systems and provide query capability on all those systems using the i2b2 web client.

Social Security Death Master File (SSDMF) Interface

The Social Security Death Master File (SSDMF) Interface is an online tool for querying the Social Security Administration's list of deceased people. SSDMF Interface enables users to log into the SSDMF, query it and download the results in a spreadsheet-friendly Comma Separated Value (CSV) format.  You must purchase a SSDMF account from the Social Security Administration, the user ID and password they provide is used to log into the SSDMF Interface, which validates your account with the SSDMF's web services.

Users can enter a person's first and last names and date of birth.  The SSDMF Interface retrieves the latest matching entry(ies) from the SSDMF web service and stores them in a CSV file. Users can alternatively upload a list of names and dates of birth.  All the names will be looked up in the SSDMF web service and all of the results will be stored in single CSV file.

Workflow Services

Galaxy

Galaxy is an open, web-based platform for data intensive biomedical research. The CVRG has deployed an instance of Galaxy within the Amazon cloud that is available for use by the community to test its features. CVRG has integrated Globus Online data transfer methods into its instance of Galaxy, as well as Bioconductor R scripts that arepart of the CRData.org analytical services. Combining these tools allows for storage, transfer and analysis of multi-scale data.

While the CVRG has integrated components into Galaxy, it also contains tools for the creation and sharing of workflows. Workflows can be written to retrieve data from one of the other data services (e.g., an instance of the ECGrid Toolkit), pass those data to an analysis service (e.g., the QT screening algorithm) and return the results to the service. These workflows can be invoked from within Galaxy or called via REST services.