ORscraper: Extract Information from Clinical Reports from 'Oncomine Reporter' and NCBI 'ClinVar'

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Authors: Samuel González
Cited by: 0

Abstract

Clinical reports generated by 'Oncomine Reporter' software contain critical data in unstructured PDF format, making manual extraction time-consuming and error-prone. 'ORscraper' provides a coherent suite of functions to automate this process, allowing researchers to parse reports, identify key biomarkers, extract genetic variant tables, and filter results. It also integrates with the NCBI 'ClinVar' API to enrich extracted data.

Fields of Study & Subjects

Biomedical Text Mining and Ontologies Genomics and Rare Diseases Cancer Genomics and Diagnostics

Publication details

Publication date
16 January 2026
Document type
Dataset