Authors:
Abderrahim Batouche
1
;
2
;
3
;
Eugen Czeizler
2
;
3
;
Miika Koskinen
4
;
Tuomas Mirtti
2
;
5
and
Antti Rannikko
2
;
6
Affiliations:
1
Doctoral Programme in Computer Science, University of Helsinki, Helsinki, Finland
;
2
Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
;
3
ICAN-Digital Precision Cancer Medicine Flagship, Helsinki, Finland
;
4
HUS Helsinki University Hospital, Helsinki, Finland
;
5
Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
;
6
Department of Urology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
Keyword(s):
Data Mining, Electronic Health Records, Missing Data, Prostate Cancer.
Abstract:
The presence of detailed clinical information in electronic health record (EHR) systems presents promising prospects for enhancing patient care through automated retrieval techniques. Nevertheless, it is widely acknowledged that accessing data within EHRs is hindered by various methodological challenges. Specifically, the clinical notes stored in EHRs are composed in a narrative form, making them prone to ambiguous formulations and highly unstructured data presentations, while structured reports commonly suffer from missing and/or erroneous data entries. This inherent complexity poses significant challenges when attempting automated large-scale medical knowledge extraction tasks, necessitating the application of advanced tools, such as natural language processing (NLP), as well as data audit techniques. This work aims to address these obstacles by creating and validating a novel pipeline designed to extract relevant data pertaining to prostate cancer patients. The objective is to exp
loit the inherent redundancies available within the integrated structured and unstructured data entries within EHRs in order to generate comprehensive and reliable medical databases, ready to be used in advanced research studies. Additionally, the study explores potential opportunities arising from these data, offering valuable prospects for advancing research in prostate cancer.
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