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Pathology reports are stored as unstructured, ungrammatical, fragmented, and abbreviated free text with linguistic variability among pathologists. For this reason, tumor information extraction requires a significant human effort. Recording data in an efficient and high-quality format is essential in implementing and establishing a hospital-based cancer registry.

This study aimed to describe implementing a natural language processing algorithm for oncology pathology reports.

An algorithm was developed to process oncology pathology reports in Spanish to extract 20 medical descriptors. The approach is based on the successive coincidence of regular expressions.

The validation was performed with 140 pathological reports. The topography identification was performed manually by humans and the algorithm in all reports. The human identified morphology in 138 reports and by the algorithm in 137. The average fuzzy matching score was 68.3 for Topography and 89.5 for Morphology.

A preliminary algorithm validation against human extraction was performed over a small set of reports with satisfactory results. This shows that a regular-expression approach can accurately and precisely extract multiple specimen attributes from free-text Spanish pathology reports. Additionally, we developed a website to facilitate collaborative validation at a larger scale which may be helpful for future research on the subject.

Juan Sebastian Moreno, MSc, Quantil SAS. Bogotá, Colombia. Centro de Analítica para Políticas Públicas. Bogotá, Colombia


Juan Carlos Bravo-Ocaña, MD, Fundación Valle del Lili; Departamento de Patología, Cali, Colombia


Alvaro José Riascos, PhD, Quantil SAS. Bogotá, Colombia. Centro de Analítica para Políticas Públicas. Bogotá, Colombia. Universidad de los Andes, Facultad de Economía. Bogotá, Colombia


Angela Regina Zambrano, MD, Fundación Valle del Lili; Departamento de Hemato-Oncología, Cali, Colombia


Diana Marcela Mendoza-Urbano, MD, Universidad Nacional de Colombia, Facultad de Medicina, Departamento de Patología, Bogotá, Colombia,Universidad Nacional de Colombia, Facultad de Medicina, Departamento de Patología, Bogotá, Colombia


Johan Felipe Garcia, PhD, Quantil SAS. Bogotá, Colombia


Sergio I Prada, MPA, PhD, Fundación Valle del Lili, Centro de Investigaciones Clínicas, Cali, Colombia. Universidad Icesi, Centro PROESA, Cali, Colombia


Moreno, J. S., Bravo-Ocaña, J. C., Riascos, A. J., Zambrano, A. R., Mendoza-Urbano, D. M., Garcia, J. F., & Prada, S. I. (2023). Automated extraction of information from free text of Spanish oncology pathology reports. Colombia Medica, 54(1), e2035300. (Original work published March 30, 2023)

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Received 2022-06-11
Accepted 2023-03-01
Published 2023-08-09