Difference between revisions of "CGS"
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=== Linked data crawler === | === Linked data crawler === | ||
+ | We use LDSpider for crawling the different components of our infrastructure | ||
− | + | * '''Purpose:''': | |
+ | ** Is able to consume and traverse the web of linked data | ||
+ | ** Aggregates both the contents of the semantic media wiki and XNAT into a central triple store. | ||
− | * | + | * '''Install LDSpider''':<br />Detailed information about LDSpider, the linked data crawler we are using, can be found here: https://github.com/ldspider/ldspider |
=== Triple Store === | === Triple Store === |
Revision as of 13:36, 9 February 2016
Overview
On this page you can find detailed information about how to build up the semantic data infrastructure that is published in:
Fetzer, A., J. Metzger, D. Katic, K. März, M. Wagner et al., "Towards an open-source semantic data infrastructure for integrating clinical and scientific data in cognition-guided surgery.", in Proc. SPIE Medical Imaging 2016 "PACS and Imaging Informatics: Next Generation and Innovations", 9789-22, (2016)
The proposed infrastructure allows you to integrate heterogneous data sets and make them available via a unified interfaced. Also the data can be annotated and integrated semantically which facilitates complex semantic queries on the data.
An overview about the components of the infrastructure is depicted in the figure below:
Following we briefly describe the components and tools of the infrastructure and how to get/install them.
Semantic data infrastructure
XNAT - A flexible data storage
The Extensible Neuroimaging Archive Toolkit (XNAT) is a flexible data storage system. It is developed at the Washington University in St. Louis and focuses on storing medical image data but is capable to handle arbitrary data as well.
- Purpose:
- Store arbitrary data like medical images, meshes, videos
- Connect with hospital PACS
- Utilize flexible interfaces to access data in a privacy compliant way
- Install XNAT:
A detailed description about how to install XNAT can be found here: https://wiki.xnat.org/display/XNAT16/XNAT+1.6+Installation+Guide
- XNAT Linked Data Wrapper:
- Utilizes the comprehensice REST API of XNAT and converts its responses into linked data
- Thus connects XNAT to the semantic data infrastructure.
- Is available here: http://surgipedia.sfb125.de/wiki/XNAT_Wrapper
- Contact Marco Nolden for detailed information
Surgipedia - A semantic media wiki
A Semantic Media Wiki is an extension to the Media Wiki that can be used as an flexible knowledge management system.
- Purpose:
- Integrate with and link to external ontologies
- Collaboratively model knowledge and ontologies
- Create semantic data annotations
- Install semantic media wiki:
A detailed description about how to install a semantic media wiki can be found here: https://www.semantic-mediawiki.org/wiki/Help:Installation
- Surgipedia:
Our semantic media wiki instance: https://surgipedia.sfb125.de
Linked data crawler
We use LDSpider for crawling the different components of our infrastructure
- Purpose::
- Is able to consume and traverse the web of linked data
- Aggregates both the contents of the semantic media wiki and XNAT into a central triple store.
- Install LDSpider:
Detailed information about LDSpider, the linked data crawler we are using, can be found here: https://github.com/ldspider/ldspider
Triple Store
A triple store is a data base which is especially designed for handling linked data from the semantic web. There are many triple store implementations available and the choice which you want to use is up to you. Here is a small selection of available triple stores:
- The one we are using: OpenLink Virtuoso
- Redland
- Apache Jena
Cognition-Guided Surgery Workbench
The CGS Workbench is an MITK-based desktop application, which provides both flexibility and extensibility for methods integration and unified interfaces to the proposed infrastructure.
Core-features of the CGS Workbench are:
- DICOM viewing
- Image processing: Segmentation, measurement, image statistics
- XNAT connection: Browse, up- and download your data from XNAT
- Triple store connection: Query / Insertion of triples
- Semantic data annotation: Create annotation files, upload annotation to XNAT or insert directly into the triple store
How to get it?
- Source code as well as binary installers can be found here: https://projects.sfb125.de (registration required)
- Or contact Marco Nolden / Jasmin Metzger