Differences

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--- members:bernard.gibaud:medirad-page [2020/11/16 14:50]
gibaud
+++ members:bernard.gibaud:medirad-page [2020/11/18 09:18] (current)
gibaud
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   * a component called **Semantic Translator**, providing a set of services to populate and query the semantic database
   * a STARDOG Triple Store, supporting the semantic database
-  * a component called **Sparklis** Portal, extending the IRDBB_UI to assist the users in building SPARQL queries
+  * a component called **SPARKLIS** Portal, extending the IRDBB_UI to assist the users in building SPARQL queries
   * a component called **Keycloak**, also provided by ITMI and b<>com providing a Single Sign-On mechanism for access control.
@@ Line 56: / Line 56: @@
 The Semantic database is an RDF graph containing RDF assertions that document the nature and provenance of all the data shared in the MEDIRAD IRDBB repository, i.e. DICOM or non-DICOM data.
 The DICOM data concern:
   * image data such as CT images, that correspond directly to irradiation events
   * image data such as SPECT or PET images, that may either correspond to irradiation events (due to the injection of a radiopharmaceutical) with some diagnostic goal, or correspond to a strategy to estimate the biodistribution of the radiopharmaceutical used in an internal radiotherapy (e.g. 131Iodine treatment of thyroïd cancer)
   * structured reports such as CT Radiation Dose Structured Reports
-  * other structured reports, e.g. implementing e-CRF documenting the internal radiotherapy treatments in WP3
+  * other structured reports, e.g. implementing e-CRF documenting the internal radiotherapy treatments in WP3.
-The non-DICOM data concern e.g.:
+The non-DICOM data concern principally:
   * voxelized dose maps calculated by Monte Carlo simulation
   * segmentation of organs and tissues of interest.
-The Semantic database is populated by the Semantic Translator, when the data files are imported into the IRDBB system.
+The Semantic database is populated by the Semantic Translator, this processing is completed during the importation of the data files into the IRDBB system.
-It is supported by the Stardog Triple store.
+The Semantic database is supported by the [[https://www.stardog.com/|Stardog Triple store]].
-The Semantic database can be queried though the IRDBB_UI web interface. Two ways are proposed:
+The Semantic database can be queried through the IRDBB_UI web interface. Two ways are proposed:
-  * use of predefined SPARQL queries
+  * using predefined SPARQL queries
-  * use of the [[http://www.irisa.fr/LIS/ferre/sparklis/osparklis.html|SPARKLIS tool]], a tool allowing the end-users to freely navigate in the RDF graph and build their own SPARQL queries. This tool was provided by [[http://people.irisa.fr/Sebastien.Ferre/|Sébastien Ferré]] (University of Rennes 1).
+  * using the Sparklis tool, a tool allowing the end-users to freely navigate in the RDF graph and build their own SPARQL queries. The [[http://www.irisa.fr/LIS/ferre/sparklis/osparklis.html|SPARKLIS tool]] was provided free of charge by [[http://people.irisa.fr/Sebastien.Ferre/|Sébastien Ferré]] (University of Rennes 1).
@@ Line 80: / Line 81: @@
 The main services concern the creation of the RDF assertions describing the nature and provenance of the DICOM and non-DICOM data, and the management of predefined SPARQL queries.
 For DICOM data, the Semantic translator translates into RDF the key DICOM metadata. For non-DICOM data, the relevant provenance metadata are provided in an XML file (non-DICOM File set descriptor) that is part of the non-DICOM File set to be imported.
-A more detailed documentation of the Semantic translator is available in xx.
-The domain covered by the predefined SPARQL queries is described in yy.
@@ Line 95: / Line 95: @@
   * Osman Ratib, ITMI, Genève
-==== Other collaborators in the development of IRDBB ====
+==== Other collaborators  ====
   * John Stratakis, University of Crete
@@ Line 111: / Line 111: @@
 ====== Technical reports ======
-  - Documentation of the ontology of the IRDBB semantic repository, Version 1.3, MEDIRAD Technical report, MS8 Milestone, 2020.
+  - Documentation of the ontology of the IRDBB semantic repository, Version 1.3, MEDIRAD Technical report, MS8 Milestone, 2020. {{:members:bernard.gibaud:mediraddocumentation-of-ontologyv1.3.pdf|pdf}}
-  - Documentation of the Semantic Translator software, Version 1, MEDIRAD Technical report, 2020.
+  - Documentation of the Semantic Translator software, Version 1, MEDIRAD Technical report, 2020. {{:members:bernard.gibaud:mediraddocumentation-of-ontologyv1.3.pdf|pdf}}
-  - Documentation of predefined SPARQL queries, Version 1, MEDIRAD Technical report, 2020.
+  - Documentation of predefined SPARQL queries, Version 1, MEDIRAD Technical report, 2020. {{:members:bernard.gibaud:mediradocumentation-of-predefined-queriesv1.0.pdf|pdf}}
@@ Line 120: / Line 121: @@
 ====== Publications ======
-  - Spaltenstein J, Roduit N, van Dooren N, Pasquier G, Brenet M, Gibaud B, Pasquier G, Mildenberger P and Ratib O. A multicentric IT platform for storage and sharing of imaging-based radiation dosimetric data. CARS 2020 Munich (Germany).
+  - Spaltenstein J, Roduit N, van Dooren N, Pasquier G, Brenet M, Gibaud B, Pasquier G, Mildenberger P and Ratib O. A multicentric IT platform for storage and sharing of imaging-based radiation dosimetric data. CARS 2020 Munich (Germany).[[https://link.springer.com/article/10.1007/s11548-020-02179-y|paper]]
-  - Gibaud B, Brenet M, Pasquier G, Vergara Gil A, Bardiès M, Stratakis J, Damilakis J, van Dooren N, Spaltenstein J, and Ratib O. A semantic database for integrated management of image and dosimetric data in low radiation dose research in medical imaging. American Medical Informatics Association (AMIA) Conference, November 2020, Chicago (USA).
+  - Gibaud B, Brenet M, Pasquier G, Vergara Gil A, Bardiès M, Stratakis J, Damilakis J, van Dooren N, Spaltenstein J, and Ratib O. A semantic database for integrated management of image and dosimetric data in low radiation dose research in medical imaging. American Medical Informatics Association (AMIA) Conference, November 2020, Chicago (USA), 492-501. {{:members:bernard.gibaud:AMIA-medirad-final.pdf|paper}} {{:members:bernard.gibaud:s71-bgibaudamia2020.pdf|slides}}
 ====== Funding ======