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* a component called **Semantic Translator**, providing a set of services to populate and query the semantic database | * 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 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. | * a component called **Keycloak**, also provided by ITMI and b<>com providing a Single Sign-On mechanism for access control. | ||
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* 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) | * 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 | * 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 | * voxelized dose maps calculated by Monte Carlo simulation | ||
* segmentation of organs and tissues of interest. | * 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). |
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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. | 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. | 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. | + | |
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* Osman Ratib, ITMI, Genève | * Osman Ratib, ITMI, Genève | ||
- | ==== Other collaborators in the development of IRDBB ==== | + | ==== Other collaborators ==== |
* John Stratakis, University of Crete | * John Stratakis, University of Crete | ||
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====== Technical reports ====== | ====== 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}} |
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====== Publications ====== | ====== 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). {{:members:bernard.gibaud:AMIA-medirad-final.pdf|paper}} {{:members:bernard.gibaud:AMIA-medirad-final.pdf|slides}} |
====== Funding ====== | ====== Funding ====== |