i2b2-onco-pg23

 

Project status: Current

Coordinator: ASST Papa Giovanni XXIII, Bergamo, IT

Field: Oncologia

Start date: September 1st, 2016

Platform: i2b2

 

Since 2017, the “vertical” project specific to the Oncology Department has been active within the i2b2 system of ASST Papa Giovanni XXIII. The project contains the data integrated in the horizontal corporate project but limited to patients with an oncological diagnosis, in particular:

  • the oncology medical record
  • hospitalisation flow of the discharged patients
  • pharmacological therapies administered and delivered
  • outpatient procedures
  • outcomes of clinical chemistry and microbiology laboratory data
  • anatomic pathology reports.

In addition, the project includes information extracted from anatomic pathology reports related to patients with breast cancer using a Text-Mining algorithm. The algorithm uses NLP (Natural Language Processing) techniques that exploits an ontology referring to breast cancer. The ontology was defined based on a reference ontology (PATHLEX) and the specific information to be extracted. During validation, the algorithm exceeded 90% accuracy. The procedure was then applied to all breast cancer reports (about 20 thousand reports).
The project also integrates specific clinical studies performed with data of patients belonging to the institute, in particular the tool is very efficient to collect data for RWE (Real-World Evidence) studies.

References:

  • Viani N, Chiudinelli L, Tasca C, Zambelli A, Bucalo M, Ghirardi A, Barbarini N, Sfreddo E, Sacchi L, Tondini C, Bellazzi R. Automatic Processing of Anatomic Pathology Reports in the Italian Language to Enhance the Reuse of Clinical Data. Stud Health Technol Inform. 2018;247:715-719. PMID: 29678054Viani N, Chiudinelli L, Tasca C, Zambelli A, Bucalo M, Ghirardi A, Barbarini N, Sfreddo E, Sacchi L, Tondini C, Bellazzi R. Automatic Processing of Anatomic Pathology Reports in the Italian Language to Enhance the Reuse of Clinical Data. Stud Health Technol Inform. 2018;247:715-719. PMID: 29678054 (link, pdf).
  • Zambelli A, Ghirardi A, Masciulli A, Sfreddo E, Porcino R, Bucalo M, Barbarini N, Chiudinelli L, Chirco A, Labianca A, Barbui T, Tondini C. Ten-years electronic phenotyping archive and automated reconstruction of her2+ breast cancer patients careflow, through the exportable, open-source i2b2 data ware-housing platform. XX Congresso Nazionale AIOM 2018. (pdf)
  • Chiudinelli L, Viani N, Zambelli A, Gabetta M, Bucalo M, Ghirardi A, Sfreddo E, Sacchi L, Tondini C, Bellazzi R. i2b2 Ontology Curation leveraging clinical notes. NETTAB 2018. (pdf)