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©Siemens Corporation, Corporate Research, Integrated Data Systems, 2009. All rights reserved. © Siemens Corporation, Corporate Research, 2009. All rights reserved.

SciPort

Fabian Moerchen, Philipp Hussels, Claus NeubauerIntegrated Data Systems, Siemens Corporation, Corporate ResearchPrinceton, NJ

©Siemens Corporation, Corporate Research, Integrated Data Systems, 2009. All rights reserved.

SciPort Integrating, sharing, and searching data and meta-data

Problem

Solution

Scientific data is highly complex and diverseStructured data such as spreadsheets and SQL databasesSemi-structured data such as documents (Word, PDF, …)Images stored in PACS or file systems (DICOM, …)Multimedia files (videos, slides, …)Raw data files with scientific measurements

Scientific databases have different formats and access protocolsSQL, XMLWeb/Grid services

There is a need to integrate and share scientific data across multiple distributed sites and organizations and make it searchable through a unified interface.

SciPortTM – a web-based platform for scientific data management Integration of data from databases, file system, and gridsRapid data acquisition of meta-data through custom web formsUnified search interface for meta-data and contentLight weight data publishing data across distributed sitesFine grained access control to the database Personalization through tagging of database contents


SciPort Modeling of domain model

Define domain model(s)Use SciPort web interface to define document templatesThe data fields support text, numbers, dates, tables, lists, files, etc.Each field can be constrained: required, min/max, drop down, etc.

Documents can be divided into

semantic sections

Data types include checkboxes, dates,

etc.

Specify values for drop down lists

Specify type and number of files that

can be attached


SciPort Example: Annotation Document

Group

Category

File

Field

Field

Multiple instances of complex records

Tables

File attachments


SciPort Modeling of permissions

Use SciPort web interface to define users and groups of users.A user has a specific role in each assigned group.A role define the permissions (read/write documents, add users, etc.)

Define users and permissions

Reader in the group MR

Administrator in the group SCR


SciPort Modeling of folders

Define folders for documentsUse SciPort web interface to define folders and subfolders.Each folder is associated with document templates.Each folder can be associated with a group of users

Folder tree to sort documents as on a personal computer

This folder can store documents from three

specific templates

By creating a group of users and assigning them to this folder, data access can be

restricted to a folder branch


SciPort Data acquisition

Authoring of documentsUse SciPort web interface to create new documents.Upload files with scientific data and associate it with meta-data.Constraints are checked to ensure high data quality.

Add rows to tables

Nested document structure

Attach DICOM images or other files


SciPort Ontology support

Ontology supportText fields can be constrained to ontologies.RadLex – Lexicon for radiologyAuto-completion with relevant terms as the user types.

Auto-completionfrom controlled

ontology vocabulary


SciPort Data integration

Import of legacy dataUse SciPort Batch Loader to populate database from folders with images and spreadsheets.Plugin of custom import modules to import data from XML or SQL databases.Unified interface to search the consolidated data through SciPort web client.

File systemimport SciPort XML

SciPortDatabase

Files

Domain model

Databaseimport SciPort XMLSQL

XMLtransformation SciPort XMLXML

SciPort Batch Loader

SciPortweb client


SciPort Searching

Flexible search interface to document databaseUse SciPort web interface to search for documents combining three types of criteria:

Keyword search over all data fieldsMeta-data search (authors, creation date, etc.)Domain search: conditions on specific data fields of domain model.

Keyword searchMeta-data search

Domain searchRestrict to folder

Paging of results


SciPort Sharing

Lightweight infrastructure for document sharingUsers can publish selected documents to a central read-only server.Users can browse the central server and receive large files from original server on demand.Shared documents are updated automatically.Templates can be shared including support for backward compatible changes.

Structured DocumentsStructured Documents

Images/FilesImages/Files

Local Server

Structured Documents

andTemplates

Central Server

Lightweight publishing of domain

data with links to attachments

Retrieve attached files of particular document

on demand



Local Server



Local Server



Local Server

User

Browsing and searching published

documents


SciPort Exporting

Export modules for documents and filesUse SciPort web interface to download documents and files as ZIP files.Export nested documents as spreadsheets with ‘flat’ structure for analysis with statistical tools or databases.Publish images and annotations to the National Biomedical Imaging Archive (NBIA) of caBIG.

SciPortDatabase

SciPortweb client

NIHClinical Trial Processor

Spreadsheets

ZIP files

SQL export

R/SAS®/Matlab®

caGRID


SciPort Technology

Data storage

Medical imaging supports

Hybrid storage strategy based on XML, SQL and file system.XML enables highly customizable modeling of scientific data with arbitrarily nested structures.IBM DB2 relational database with pureXML technology for XML indexing enables storage of XML documents with efficiency, scalability, and security of a SQL databaseStoring attachments in the file system keeps the database small and enables transparent access and backup of file for administrative users on the server.

Highly interactive AJAX web based user interfaceSecure access with HTTPS and encrypted passwords.Use of proven scalable web technologies (Tomcat, JSP, JBoss, web services)

Web application

Indexing of headers and thumbnail generation for DICOM images.Integration and indexing of image annotations in AIM format.HIPAA: anonymization, encrypted passwords and protocols.caGRID: publish images and annotation to the NBIA (National Biomedical Imaging Archive)


SciPort Use cases

Collaboration management

Research in emerging imaging modalities

Siemens H USA has many collaborations with hospitals.Siemens provides imaging equipment and obtains acquisitions, case reports, evaluation reports, publications.SciPort is used by several imaging divisions to manage this data centrally for research, marketing, and compliance.

SciPort can be used to rapidly perform data collection for (research) clinical trials.Setup a single server accessible to all clinical partners and design questionaires in SciPort.Automated upload of large amounts of imaging data using the SciPort batch loader.

Clinical trials data collection

Researchers in emerging imaging modalities need to compare results with conventional methods. Need to pool data from multiple research sites.SciPort can manage (anonymized) patient information, DICOM images and non-standard formats in one system.


SciPort Road map summary

Hot new features on the road map

Data management

SciPort flash client with even more interaction and visualization, see next slides.Wolfram-alpha like search with statistical summaries of search results.Integration with SCR’s Extensible Imaging Platform (XIP), see next slides.Integration with SCR’s ProFound for data-driven comparative effectiveness researchIntegration with Algorithm Validation Tool (AVT), see next slides

Evaluate variability of image annotationsIntegration with data analysis tools

R, SAS, MatlabSCR’s iKDD™ (Interactive Knowledge Discovery and Data Mining)

Automatic synchronization of distributed servers for faster access of remote data.Alternative P2P architecture for searching and tagging.More interoperability with standards such as PACS, HL7, caGRID, etc.Single-sign on with LDAP etc.

Connecting, publishing and sharing

Support drafts and versioning of documents generating an audit trail for HIPAA compliance.Data quality reporting (number of missing values per template / folders)


SciPort Road map: Flash client

WYSIWYG form design with drag & drop

Flash technology for web clients enables more interactivity, visualization and improved browser compatibility.


SciPort Road map: XIP integration

XIP is an open source framework and platform for rapidly developing medical imaging applications that are "plug-and- play" across multiple computing environments. It offers an extensible set of modular objects for researchers to develop and evaluate software solutions for research and clinical problems. XIP also provides an integrated development environment (IDE) for imaging software development through the use of modular Visual Programming, without the need to write and compile any code.

SciPortDatabase

Results

Annotations

Images

SCR ImagingGianluca Paladini [email protected]

SciPort can provide images to XIP and derived annotations and results.

mailto:[email protected]


SciPort Road map: ProFound integration

Modular construction of disease screening workflowsUsers can select and connect disease, screening, and treatment modules or select pre-constructed workflows.

Rapid customization of model parametersUsers edit selected parameters, such as the sensitivity, specificity, and cost of a module.

1- and 2-D Sensitivity analysisEnables the user to explore cost- effectiveness over a range of parameter values

SCR IDSGayle Wittenberg [email protected]

ProFound is an IT framework for comparative effectiveness modeling, simulation, optimization and visualization of complex healthcare workflows. ProFound includes modules describing disease progression, screening, and treatment of patients and help to evaluate workflows regarding life-years saved, quality of life, and cost.

SciPortDatabase

Results

Models

EHR

SciPort can provide high quality electronic health records to ProFound to perform data-driven comparative effectiveness analysis and store ProFound workflow definitions, workflow parametrizations, trained workflow models, and effectiveness results back into SciPort.



SciPort Road map: AVT integration

SCR SEScott Keneman [email protected]

SciPortDatabase

Results

Models

Images

AVT is a project to develop caBIG community tools for analyzing the variabilility of annotations. The vision of AVT is to facilitate comparison of annotation methods from different research groups by implementing an efficient workflow and infrastructure for statistical analysis of annotations. The SciPort team is implementing the database components of AVT.

Annotations

SciPort can provide images and annotations from the electronic health records containing additional meta-data directly to AVT to utilize the statistical analysis and store results (not a current capability of AVT) for archiving and reporting.



SciPort Road map: iKDD™ integration

Siemens CT SE 5Bernd Wachmann [email protected]

iKDD™ is a platform for workflow based data mining and optimization. Users can compose complex workflows of data processing operators including preprocessing, feature selection, predictive modeling.

SciPortDatabase

Results

Models

EHR

SciPort can provide high quality integrated electronic health records including quantitative features derived from images with XIP or other tools to train predictive models. Results such as ROC curves can be stored back into SciPort.



SciPort Contact

Fabian Moerchen, Ph.D.

Siemens CorporationCorporate ResearchIntegrated Data Systems755 College Road East08540 Princeton, NJ, USATel.: +1 (609) 734-3529Fax: +1 (609) 734-3346Mobile: +1 (609) 481-9712 [email protected]