2
|
Scapicchio C, Gabelloni M, Forte SM, Alberich LC, Faggioni L, Borgheresi R, Erba P, Paiar F, Marti-Bonmati L, Neri E. DICOM-MIABIS integration model for biobanks: a use case of the EU PRIMAGE project. Eur Radiol Exp 2021; 5:20. [PMID: 33977357 PMCID: PMC8113005 DOI: 10.1186/s41747-021-00214-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
PRIMAGE is a European Commission-financed project dealing with medical imaging and artificial intelligence aiming to create an imaging biobank in oncology. The project includes a task dedicated to the interoperability between imaging and standard biobanks. We aim at linking Digital imaging and Communications in Medicine (DICOM) metadata to the Minimum Information About BIobank data Sharing (MIABIS) standard of biobanking. A very first integration model based on the fusion of the two existing standards, MIABIS and DICOM, has been developed. The fundamental method was that of expanding the MIABIS core to the imaging field, adding DICOM metadata derived from CT scans of 18 paediatric patients with neuroblastoma. The model was developed with the relational database management system Structured Query Language. The integration data model has been built as an Entity Relationship Diagram, commonly used to organise data within databases. Five additional entities have been linked to the “Image Collection” subcategory in order to include the imaging metadata more specific to the particular type of data: Body Part Examined, Modality Information, Dataset Type, Image Analysis, and Registration Parameters. The model is a starting point for the expansion of MIABIS with further DICOM metadata, enabling the inclusion of imaging data in biorepositories.
Collapse
Affiliation(s)
- Camilla Scapicchio
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.
| | - Michela Gabelloni
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Sara Maria Forte
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Leonor Cerdá Alberich
- Biomedical Imaging Research Group (GIBI230), La Fe Health Research Institute, Valencia, Spain
| | - Lorenzo Faggioni
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Rita Borgheresi
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Paola Erba
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Fabiola Paiar
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Luis Marti-Bonmati
- Medical Imaging Department, La Fe University and Polytechnic Hospital & Biomedical Imaging Research Group (GIBI230), La Fe University and Polytechnic Hospital and Health Research Institute, Valencia, Spain
| | - Emanuele Neri
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| |
Collapse
|
3
|
Martí-Bonmatí L, Alberich-Bayarri Á, Ladenstein R, Blanquer I, Segrelles JD, Cerdá-Alberich L, Gkontra P, Hero B, García-Aznar JM, Keim D, Jentner W, Seymour K, Jiménez-Pastor A, González-Valverde I, Martínez de Las Heras B, Essiaf S, Walker D, Rochette M, Bubak M, Mestres J, Viceconti M, Martí-Besa G, Cañete A, Richmond P, Wertheim KY, Gubala T, Kasztelnik M, Meizner J, Nowakowski P, Gilpérez S, Suárez A, Aznar M, Restante G, Neri E. PRIMAGE project: predictive in silico multiscale analytics to support childhood cancer personalised evaluation empowered by imaging biomarkers. Eur Radiol Exp 2020; 4:22. [PMID: 32246291 PMCID: PMC7125275 DOI: 10.1186/s41747-020-00150-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/24/2020] [Indexed: 03/12/2023] Open
Abstract
PRIMAGE is one of the largest and more ambitious research projects dealing with medical imaging, artificial intelligence and cancer treatment in children. It is a 4-year European Commission-financed project that has 16 European partners in the consortium, including the European Society for Paediatric Oncology, two imaging biobanks, and three prominent European paediatric oncology units. The project is constructed as an observational in silico study involving high-quality anonymised datasets (imaging, clinical, molecular, and genetics) for the training and validation of machine learning and multiscale algorithms. The open cloud-based platform will offer precise clinical assistance for phenotyping (diagnosis), treatment allocation (prediction), and patient endpoints (prognosis), based on the use of imaging biomarkers, tumour growth simulation, advanced visualisation of confidence scores, and machine-learning approaches. The decision support prototype will be constructed and validated on two paediatric cancers: neuroblastoma and diffuse intrinsic pontine glioma. External validation will be performed on data recruited from independent collaborative centres. Final results will be available for the scientific community at the end of the project, and ready for translation to other malignant solid tumours.
Collapse
Affiliation(s)
- Luis Martí-Bonmatí
- Medical Imaging Department, La Fe University and Polytechnic Hospital & Biomedical Imaging Research Group (GIBI230) at La Fe University and Polytechnic Hospital and Health Research Institute, Av. Fernando Abril Martorell 106, 46026, Valencia, Spain.
| | - Ángel Alberich-Bayarri
- Quantitative Imaging Biomarkers in Medicine, QUIBIM SL, Edificio Europa, Av. de Aragón, 30, Planta 12, 46021, Valencia, Spain
| | | | - Ignacio Blanquer
- Instituto de Instrumentación para Imagen Molecular (I3M), Universitat Politècnica de València (UPV), c\ Camino de Vera s/n, 46022, Valencia, Spain
| | - J Damian Segrelles
- Instituto de Instrumentación para Imagen Molecular (I3M), Universitat Politècnica de València (UPV), c\ Camino de Vera s/n, 46022, Valencia, Spain
| | - Leonor Cerdá-Alberich
- Biomedical Imaging Research Group (GIBI230), La Fe Health Research Institute, Av. Fernando Abril Martorell 106, Torre E, 46026, Valencia, Spain
| | - Polyxeni Gkontra
- Biomedical Imaging Research Group (GIBI230), La Fe Health Research Institute, Av. Fernando Abril Martorell 106, Torre E, 46026, Valencia, Spain
| | - Barbara Hero
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - J M García-Aznar
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, Universidad de Zaragoza, Zaragoza, Spain.,Aragón Institute of Engineering Research, Zaragoza, Spain
| | - Daniel Keim
- Department of Computer Science, University of Konstanz, Konstanz, Germany
| | - Wolfgang Jentner
- Department of Computer Science, University of Konstanz, Konstanz, Germany
| | | | - Ana Jiménez-Pastor
- Quantitative Imaging Biomarkers in Medicine, QUIBIM SL, Edificio Europa, Av. de Aragón, 30, Planta 12, 46021, Valencia, Spain
| | - Ismael González-Valverde
- Quantitative Imaging Biomarkers in Medicine, QUIBIM SL, Edificio Europa, Av. de Aragón, 30, Planta 12, 46021, Valencia, Spain
| | - Blanca Martínez de Las Heras
- Paediatric Oncology Unit, La Fe University and Polytechnic Hospital, Av. Fernando Abril Martorell 106, Torre G, 2 Floor, 46026, Valencia, Spain
| | - Samira Essiaf
- European Society for Paediatric Oncology, Brussels, Belgium
| | - Dawn Walker
- Department of Computer Science and Insigneo Institute of In Silico Medicine, University of Sheffield, Regent Court, 211 Portobello, Sheffield, UK
| | - Michel Rochette
- Simulation, Modelling and Engineering Software, Ansys Group, Montigny-le-Bretonneux, France
| | - Marian Bubak
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | - Jordi Mestres
- Chemotargets S.L., Carrer de Baldiri Reixac, 4-8 TI05A7 Torre I, planta 5, A7, 08028, Barcelona, Spain
| | - Marco Viceconti
- Department of Industrial Engineering, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Gracia Martí-Besa
- Biomedical Imaging Research Group (GIBI230), La Fe Health Research Institute, Av. Fernando Abril Martorell 106, Torre E, 46026, Valencia, Spain
| | - Adela Cañete
- Paediatric Oncology Unit, La Fe University and Polytechnic Hospital, Av. Fernando Abril Martorell 106, Torre G, 2 Floor, 46026, Valencia, Spain
| | - Paul Richmond
- Department of Computer Science and Insigneo Institute of In Silico Medicine, University of Sheffield, Regent Court, 211 Portobello, Sheffield, UK
| | - Kenneth Y Wertheim
- Department of Computer Science and Insigneo Institute of In Silico Medicine, University of Sheffield, Regent Court, 211 Portobello, Sheffield, UK
| | - Tomasz Gubala
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | - Marek Kasztelnik
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | - Jan Meizner
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | - Piotr Nowakowski
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | | | - Amelia Suárez
- Matical Innovation, Calle de Torija, 5, 28013, Madrid, Spain
| | - Mario Aznar
- Matical Innovation, Calle de Torija, 5, 28013, Madrid, Spain
| | - Giuliana Restante
- Department of Translational Research, University of Pisa, Chair Radiodiagnostica 3, Pisa University Hospital, Via Roma 67, 56126, Pisa, Italy
| | - Emanuele Neri
- Department of Translational Research, University of Pisa, Chair Radiodiagnostica 3, Pisa University Hospital, Via Roma 67, 56126, Pisa, Italy
| |
Collapse
|