The ONCO-I2b2 project: Integrating biobank information and clinical data to support translational research in oncology

Daniele Segagni; Valentina Tibollo; Arianna Dagliati; Leonardo Perinati; Alberto Zambelli; Silvia Priori; Riccardo Bellazzi

doi:10.3233/978-1-60750-806-9-887

The ONCO-I2b2 project: Integrating biobank information and clinical data to support translational research in oncology

Daniele Segagni, Valentina Tibollo, Arianna Dagliati, Leonardo Perinati, Alberto Zambelli, Silvia Priori, Riccardo Bellazzi

Istituti Clinici Scientifici Maugeri Spa – Società Benefit

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

The University of Pavia and the IRCCS Fondazione Salvatore Maugeri of Pavia (FSM), has recently started an IT initiative to support clinical research in oncology, called ONCO-i2b2. ONCO-i2b2, funded by the Lombardia region, grounds on the software developed by the Informatics for Integrating Biology and the Bedside (i2b2) NIH project. Using i2b2 and new software modules purposely designed, data coming from multiple sources are integrated and jointly queried. The core of the integration process stands in retrieving and merging data from the biobank management software and from the FSM hospital information system. The integration process is based on a ontology of the problem domain and on open-source software integration modules. A Natural Language Processing module has been implemented, too. This module automatically extracts clinical information of oncology patients from unstructured medical records. The system currently manages more than two thousands patients and will be further implemented and improved in the next two years.

Original language	English
Title of host publication	Studies in Health Technology and Informatics
Pages	887-891
Number of pages	5
Volume	169
DOIs	https://doi.org/10.3233/978-1-60750-806-9-887
Publication status	Published - 2011
Event	23rd International Conference of the European Federation for Medical Informatics, MIE 2011 - Oslo, Norway Duration: Aug 28 2011 → Aug 31 2011

Other

Other	23rd International Conference of the European Federation for Medical Informatics, MIE 2011
Country/Territory	Norway
City	Oslo
Period	8/28/11 → 8/31/11

Keywords

Biobanks
Hospital information system integration
I2B2
Natural language processing
Oncology research
Translational research

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Health Information Management

Access to Document

10.3233/978-1-60750-806-9-887

Cite this

Segagni, D, Tibollo, V, Dagliati, A, Perinati, L, Zambelli, A, Priori, S & Bellazzi, R 2011, The ONCO-I2b2 project: Integrating biobank information and clinical data to support translational research in oncology. in Studies in Health Technology and Informatics. vol. 169, pp. 887-891, 23rd International Conference of the European Federation for Medical Informatics, MIE 2011, Oslo, Norway, 8/28/11. https://doi.org/10.3233/978-1-60750-806-9-887

@inproceedings{03c60e58342c480f947f9f9004f60499,

title = "The ONCO-I2b2 project: Integrating biobank information and clinical data to support translational research in oncology",

abstract = "The University of Pavia and the IRCCS Fondazione Salvatore Maugeri of Pavia (FSM), has recently started an IT initiative to support clinical research in oncology, called ONCO-i2b2. ONCO-i2b2, funded by the Lombardia region, grounds on the software developed by the Informatics for Integrating Biology and the Bedside (i2b2) NIH project. Using i2b2 and new software modules purposely designed, data coming from multiple sources are integrated and jointly queried. The core of the integration process stands in retrieving and merging data from the biobank management software and from the FSM hospital information system. The integration process is based on a ontology of the problem domain and on open-source software integration modules. A Natural Language Processing module has been implemented, too. This module automatically extracts clinical information of oncology patients from unstructured medical records. The system currently manages more than two thousands patients and will be further implemented and improved in the next two years.",

keywords = "Biobanks, Hospital information system integration, I2B2, Natural language processing, Oncology research, Translational research",

author = "Daniele Segagni and Valentina Tibollo and Arianna Dagliati and Leonardo Perinati and Alberto Zambelli and Silvia Priori and Riccardo Bellazzi",

year = "2011",

doi = "10.3233/978-1-60750-806-9-887",

language = "English",

isbn = "9781607508052",

volume = "169",

pages = "887--891",

booktitle = "Studies in Health Technology and Informatics",

note = "23rd International Conference of the European Federation for Medical Informatics, MIE 2011 ; Conference date: 28-08-2011 Through 31-08-2011",

}

TY - GEN

T1 - The ONCO-I2b2 project

T2 - 23rd International Conference of the European Federation for Medical Informatics, MIE 2011

AU - Segagni, Daniele

AU - Tibollo, Valentina

AU - Dagliati, Arianna

AU - Perinati, Leonardo

AU - Zambelli, Alberto

AU - Priori, Silvia

AU - Bellazzi, Riccardo

PY - 2011

Y1 - 2011

N2 - The University of Pavia and the IRCCS Fondazione Salvatore Maugeri of Pavia (FSM), has recently started an IT initiative to support clinical research in oncology, called ONCO-i2b2. ONCO-i2b2, funded by the Lombardia region, grounds on the software developed by the Informatics for Integrating Biology and the Bedside (i2b2) NIH project. Using i2b2 and new software modules purposely designed, data coming from multiple sources are integrated and jointly queried. The core of the integration process stands in retrieving and merging data from the biobank management software and from the FSM hospital information system. The integration process is based on a ontology of the problem domain and on open-source software integration modules. A Natural Language Processing module has been implemented, too. This module automatically extracts clinical information of oncology patients from unstructured medical records. The system currently manages more than two thousands patients and will be further implemented and improved in the next two years.

AB - The University of Pavia and the IRCCS Fondazione Salvatore Maugeri of Pavia (FSM), has recently started an IT initiative to support clinical research in oncology, called ONCO-i2b2. ONCO-i2b2, funded by the Lombardia region, grounds on the software developed by the Informatics for Integrating Biology and the Bedside (i2b2) NIH project. Using i2b2 and new software modules purposely designed, data coming from multiple sources are integrated and jointly queried. The core of the integration process stands in retrieving and merging data from the biobank management software and from the FSM hospital information system. The integration process is based on a ontology of the problem domain and on open-source software integration modules. A Natural Language Processing module has been implemented, too. This module automatically extracts clinical information of oncology patients from unstructured medical records. The system currently manages more than two thousands patients and will be further implemented and improved in the next two years.

KW - Biobanks

KW - Hospital information system integration

KW - I2B2

KW - Natural language processing

KW - Oncology research

KW - Translational research

UR - http://www.scopus.com/inward/record.url?scp=83055179447&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=83055179447&partnerID=8YFLogxK

U2 - 10.3233/978-1-60750-806-9-887

DO - 10.3233/978-1-60750-806-9-887

M3 - Conference contribution

C2 - 21893874

AN - SCOPUS:83055179447

SN - 9781607508052

VL - 169

SP - 887

EP - 891

BT - Studies in Health Technology and Informatics

Y2 - 28 August 2011 through 31 August 2011

ER -

The ONCO-I2b2 project: Integrating biobank information and clinical data to support translational research in oncology

Abstract

Other

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this