Evidence map›Paper›PMID 42768362›Full record

ArticleBMC research notes2026

A domain-specific annotation framework and expert-annotated corpus for structured analysis of German HNSCC pathology reports.

Sebastian Gubik, Franziska Seger, Andreas Vollmer, Marius Hörner, Tobias Renner, Luca Kohlhepp, Marc Manthey, Urs Müller-Richter, Alexander Kübler, Stephan Hackenberg and 1 more

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Article in BMC research notes, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

11 authors.

Sebastian GubikDepartment of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany. gubik_s@ukw.de.ORCID https://orcid.org/0009-0006-7312-5519
Franziska SegerDepartment of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.
Andreas VollmerDepartment of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.
Marius HörnerDepartment of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.
Tobias RennerDepartment of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.
Luca KohlheppCAIDAS (Center of AI and Data Science), University Würzburg, Würzburg, Germany.
Marc MantheyInstitute of Pathology, University of Würzburg, Würzburg, Germany.
Urs Müller-RichterDepartment of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.
Alexander KüblerDepartment of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.
Stephan HackenbergDepartment of Otorhinolaryngology, Plastic, Aesthetic, and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Würzburg, Germany.
Stefan HartmannDepartment of Oral and Maxillofacial Plastic Surgery - Head and Neck surgery, University Hospital of Würzburg, Pleicherwall 2, Würzburg, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

objectiveTo develop and empirically characterize a domain-specific, block-structured annotation schema and an expert-annotated reference corpus for German-language head and neck squamous cell carcinoma (HNSCC) pathology reports. RESULTS DESCRIPTION: We retrieved 631 pathology reports from 145 patients treated at University Hospital Würzburg between January 2021 and March 2024 and split them at the patient level into training, validation, and evaluation subsets. Reports were manually annotated using a hierarchical, span-based schema supporting overlapping and nested annotations. The resulting corpus contains 45 unique labels organized into clinically meaningful blocks and an average of 37-39 annotations per report across subsets. Label frequencies and normalized category distributions were broadly comparable across the three subsets. Fine-grained labels were predominantly applied within their designated blocks, indicating adherence to the intended block structure. The corpus provides a domain-specific reference resource for developing and evaluating structured information-extraction approaches for German HNSCC pathology reports.

Indexed as

Data MiningHead and Neck NeoplasmsNatural Language ProcessingSquamous Cell Carcinoma of Head and NeckGermanyHumansAnnotation schemaClinical natural language processingGerman medical textsHead and neck cancerInformation extractionMedical text miningPathology reportsTNM classification

Identifiers

PMID42768362
PMCPMC13595725

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.